I’ve done a few of these.. It’s important to try to cover the whole screen with the wipe for at least a couple frames, although sometimes it happens so quick that full screen coverage may not be necessary. To make it easier in FCP, try to time the wipe so it covers the screen right in the middle of the transition. The longer the coverage, the easier it will be to place the wipe over the footage in FCP.
Make use of the transparency switch under the composition viewer to make sure you have transparency when you need it. As for output, just make sure you render RGB + alpha in the Output Module settings. Of course, you will have to use a codec that supports alpha channels, like the animation codec.
Hope this helps!
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8core MacPro, 3.0 GHZ, 10GB RAM, OSX 10.5.2
DualCore G5 2.0 GHZ, 2GB RAM, OSX 10.4.11
AE7 on both for now.