How To Add Media Layers

This tutorial will shed some light on how to go about adding media elements as a layer to appear above a base clip.

First, we need to understand some of the fundamentals.
Base Element: This refers to any media file or source that has been added directly to a playlist and can be played out on their own. (standard playlist entry.) (z-order 0)
Layer Element: This refers to an element that will be associated only in conjunction with the playing of its base clip and will appear above it. (z-order 1+)
Z-Order: Refers to the order of objects along the Z-axis. Z refers to the axis perpendicular to X and Y. One can think of layers as a series of planes parallel to the surface of the monitor. The layers are therefore stacked along the Z-axis, and the Z-Order information thus specifies the bottom-to-top ordering of the layers above the base element (layer 0).
Timeline: A timeline is a graphical depiction of media elements sitting on individual tracks and where they sit within a span of time.
Limits and ground rules:
The clock that drives the timeline is a media clock generated by the base element. Since the base element supply’s the clock, the only media types that can have layers on top of them are either video or audio type clips. Still, images or live capture does not run on a media clock, hence those elements not qualify. If you try to run a layer on top them, those layers will never appear because there is no ticking clock to drive that trigger needed to start it.
The total length of a timeline is determined by the overall duration of the base media element. If you add another video or audio clip as a layer and the clip is longer in duration, then the base element the layer element will be truncated to fit within the base element’s duration.
NOTE: You will see a message box appear informing you of this discrepancy.
Maximum number of tracks AVP-V2 can handle including the base element is five.
NOTE: Keep in mind that since AVP does not re-render elements into a single video clip but instead runs each element on their own, every element including layers increases the memory, CPU & GPU burden on the local computer. Be sure that before attempting to add the max number of layers your computer qualifies and can handle that much load.  Refer to Suggested Minimum Requirements and see if your system qualifies.
Any layer that is not set to run in lockstep with its base (sync enabled) cannot start at the same time as the base element. By default, AVP will automatically ensure that any none sync layer will not be able to position its start point less than 15 frames after the start of the base clip. This is needed to allow time for internal events triggered by ticks of the base clip’s media clock to begin. Without this gap, there is a chance that the layer element may never be triggered.
There are two forms of synchronization. The first isn’t in the true since of “In Sync” rather the element free runs using its own clock, or in the case of live capture and stills simply appear on the screen. This is referred to as running async. Synchronization here is the fact that we are controlling the precise moment in time to which it will appear on screen. For any elements that were not originally rendered to the exact same frame rate as the base clip must be run async. The second is where we instruct the moving layer element to plug directly into the base element’s media clock. Now both streams are triggered to display their next frames on the exact same tick. It is recommended that that this only be employed when the individual media elements were created to work together as one. 
How to add a layer:
Before we can add layers, we fist need the base element:
Click on the “ADD” button. This will bring up another dialog. Now select the media file. Remember it can only be either a video or audio type file.
Now click on the Layer button for that clip.   This will cause a separate data table to appear.
Click on the “+Element” link at the bottom left of the layer data table and using the Media Selection Tool select a file to serve as a layer. This can be any of the four different media types.
NOTE: You can also add elements by dragging a file from Windows file explorer and drop it directly onto the layer list.
You will now see a new entry in the layer data list as well as an added track to the timeline.
For this example we added a lower third type video file.
In the case of a still image or live capture, the graphic icon will span the entire length of the timeline. Now if you do not wish to see this image overlay for the entire duration you can grab the red bar on either end and drag them to the desired time point within the timeline’ bounds. The left side determines when the element will appear, and the right is when it will disappear. (punch in and punch out) If you wish you can type the time directly into the layer’s respective columns of the layer data list.
NOTE: For motion elements such as a video or audio track, when added their icon length is in relationship to its native duration. If the element’s duration is longer then the base, the layer clip will be truncated to fit and you will see this prompt:
Let’s go back now to the data list. In each row, there are many of the same columns found in the main playlist but for layers, there is now an “Enable” and “Sync” checkbox. The enable to determine whether the layer will appear when triggered. The sync is what we use to instruct the layer to use the base elements media clock.
The “Start Time” column displays the moment when the layer will appear on the screen. You can type in values here if you wish otherwise dragging the element's icon in the timeline will set this automatically.
The rest should be self-explanatory however I would like to discuss how looping works with a motion layer element. If this set the element's icon on the timeline behaves a little differently. You can still control when the looping element will end and disappear. Simply grab the red bar at icons right edge and drag it out to the desired end. Now the clip will continue to loop for that duration and then fade away.
This screen cap shows that we dragged the layer file to start at later time point. The scrub bar shows that it will appear on screen 42 seconds after the start of the base clip.
You may also notice the gray areas to each side of the icon. The entire icon represents the native length of the file where the gray areas represent the amount time that has been trimmed off after setting both a punch in and out point. Just so you know the layer will not appear on screen until reaches the punch in point.
Here we added a PNG image file. Note that since the file as no clock its icon fills the whole timeline. As mentioned before simply drag its in and out point to set when it appears and disappears. 
Audio Concerns:
Audio level on every video and audio element within the entire playlist, layer, and base can be controlled separately as well as be assigned to any available audio output. Care needs to be given as to whether the audio output from a layer is even desired. If not be sure to mute it by clicking on the element’s speaker button. NOTE: This button is disabled on all still image and live capture elements.
Property Settings: 
Click on the setting button and use the same settings control window to tailor your element. This is especially important for layers because just like any other element when first added they will stretch to full screen.
Since all layers will have a higher z-order then its base, If the layer’s geometry is not adjusted in any way, when triggered it may conceal your base element from view entirely.   
We now know that the base element is layer 0 and cannot be changed however the z-order for layers can be changed. Simply click and drag either the element's icon in the timeline or its row in the data list, up to increase its index or down to lower it.
The rest now is up to you and your creativity.