When I am using FC and AE, it is usually doing effects work in AE.
The following mostly applies to using final cut 7 or earlier:
First I export an XML of the FC project. If it is just 1 or 2 pieces of video that need work, I just look up the time code for the clips, and import just those clips into AE. Then in AE trim them and apply the effects.
Otherwise I use a plug in to import the XML file into AE. I don't recall which one I have installed at the moment, but google and you will find several options. Odds are any transitions, effects, etc. are not going to come over properly. Don't put in transitions or effects in FC until after you have finished the AE work if you can keep from it. Once the project has pulled up in AE I precomose the clips I need to work on. Add Effects, then render out raw/uncompressed mov files or an image sequence depending on the project and established workflow.
Never use a lossy format for a master file. Sometimes you can get away with prores or Avid DNxHD, but if you can try to use a loss-less format. I also don't export audio from AE. There is no need as the audio will be in the project file.
I always export each clip on its own unless AE is being used to add a transition.
Finally in FC I pull in the new files and lay them on a track above the old files. This way nothing is lost. It is a totally non-destructive work flow.
When adding effects or cc in AE I usually add 8-10 handle frames. When working on a project I am not editing I always work out with the editor how many handle frams they want and always try to use that exact number. If I don't use that number of handle frames on a clip I make sure they get that information. If it is a clip where I know or suspect there will be a transition I make sure there are enough handle frames for the transition.
It is kinda late so I hope I didn't type too much gibberish.
If you are using final cut x, you will still export an xml file, but instead of using a plug in in AE to import the file, you will want to use a program called Clip Exporter. There are video tutorials on the web for using it. Just google it. Note the Clip Exporter may require you to do some prepwork in FC before exporting the xml file.
hope that helps
