Create an alpha channel in the Photoshop image either inside or outside the logo area.
You can use any alpha channel image (a Title, a Photoshop image with alpha, etc) to cut a HOLE (in it’s exact shape) and “Fill” it with other moving (or static) video… all “keyed over” another video track.
V3: Fill clip (what you want to be “inside” alpha)
– Select (highlight) THIS clip on V3, then:
Modify (menu) > Composite Mode > Travel Matte – Alpha
V2: Any “Alpha-channeled” clip (or title generator)
V1: Background clip (will be seen outside the “hole(s)”)
If you end up with the “reverse” of what you want, swap the clips on V1 and V3.
Remember to change the settings (Modify (menu) > Composite Mode > Travel Matte – Alpha) on the clip that is now on V3.
You can move/expand/reposition the V2 clip or even use it as a custom “wipe”.