It depends on how you’re editing. Is your FCP project 24 fps or 30 fps? When you capture in FCP, it will capture 30 fps with a pulldown unless you tell it to remove the pulldown and set the project to 24 or 23.9. Bring the footage into AE and make the comp equal the frame rate of the video. Don’t forget to field interpret lower field first. When you render, make the output fps match the comp rate, though I’m pretty sure it does this by default anyway.
The cleanliness of the video has nothing to do with the frame rate. It has to do with the codec and quality settings. This will get a little confusing but stay with me… When you render your composition (make movie) in AE, you have to choose a codec (selected in output settings in the render queue). There’s also a quality slider under options. When I’m working in AE I generally export the clip from FCP so it creates new media for me to work with in AE. When I export, I use the Animation codec because it’s a lossless codec. You won’t increase quality, but you’ll keep the footage from degrading any further as your renders pile up. You can simply open DV footage native in AE, but you’ll be working in DV. Every time you render (by selecting make movie) a comp, it will re-compress the footage and degrade it a little. The downside to the Animation codec workflow is that once you re-import into FCP, you have to render the clip in the timeline back to DV before it will play, whereas DV will play native. Make sense? Every time you make a movie in DV, you re-compress the media, making it less clean than before you rendered. Not bad for one or two generations (indeed you will have one compression even using Animation because you have to render back to DV in FCP), but as the passes pile up in DV, as you work with a rendered comp inside of another rendered comp, you’ll see a difference over time. With the Animation codec, you can in theory make a thousand nested movies and never lose any data.
Other things to watch for is make sure you have all of your comp layers set to full resolution. The default layer setting is draft mode. You can create a preset for your renders to make everything render at full resolution. If you don’t, you have to remember to change the layer setting manually every time you render.
-mjd