Hi Spencer…
If what you are saying is that you GIF’s look OK in PPro and they animate in PPro ok, but you need to export them in a way that use as elements in PPro later, then really your choice for these “intermediate clips” is DV…because this will offer the compatibility with PPro that you can easily intyeract with and playback…the method of export is different between CS3 and CS4…but if you are able to get to AVI, then you can choose the Microsoft DV AVI as the codec.
I would note that the DV codec isn’t always the friendliest to graphics….An alternative might be to choose “uncompressed” from the AVI codecs…the problem with this is that these files are bigger in data size and require a bit more umph from you disk drive to play back during subsequent editing….but as a intermediate to use on your timeline, should hold up in terms of quality until you output your final MPEG file.
IF you have the option, remember that Sequences, even multi-layer sequences can be used “clips.” You simply take the sequence icon from the Project panel and lay it on the track of another sequence…
This let’s you leave then “unrendered” until the last “output” phase of your project.
You might consider this to try to preserve the quality as much as possible….
How’s that?
Alex