If I understand you correctly you are trying to get a moving logo over a video background. Is the animation of the logo created in AE?
Depending on the version of the Media 100 system you are working on there are several ways to do that.
If your Media 100 i system (I guess you are speaking about a Media 100 i system) is running on OSX, I would at first suggest installing the software codec on your system. This will speed up AE rendering dramatically.
If you have AfterEffects installed freshly on the system, you need to install the AE import filter into your AE folder. Inside your Media 100 i folder there is a folder named “AfterEffects plugin” or something similar. Copy the file that is in this folder to the AE folder->plunins->standard->format->fpf.
Now if you export a timeline from Media 100 i (File->”export to AfterEffects” in Media 100 i) you can import that into AE, keeping all your clips intact, so that you can extend them.
Or you can export your timeline as a by-reference file (in Media 100 i, select your timeline and choose File->export; there select video and audio if you need it, and select “By Reference”). This will create a ref file that has links to your original media files. This file can be imported into AE as a long clip; e.g. as the background for your logo.
Another way would be to render out your logo from AE into Media 100 i codec. Make sure that you render into Media 100 PAL/NTSC or PAL720/NTSC720, depending on your timeline settings, and set depth to over 16million colors to include an alpha channel. Also make sure that you render out RGB+alpha, straight from AE. If you now place this clip in the G track and render that over the video in Media 100 i, the logo should be keyed over your video with its alpha channel.
Media 100