The green bar at the top indicates which part of the video has been rendered in RAM, so if you press "0", you prompt a RAM preview and you should see your "work" area fill up with green. (showing you how much of the work area has been rendered into ram)
If you enable disk caching/scratch disk, you'll see a blue bar on occasion. (this indicate which part of your timeline has been rendered onto your temporary scratch disk area or your hard drive)
About the choppy footage. To tell the truth I would like to know the best way to use time remapping. At the moment I try to avoid using it, and if I do it will be in mutiples. such as 200%, 75%, 50%.
Hope that helps, and hope you get a more comprehensive answer on the time question.
What is the frame rate of the sequence in FCP?
What is the frame rate of the clip as rendered out of FCP?
What is the frame rate of the clip as imported into AE? (look in the project window)
What is the frame rate of the comp in AE?
What is the frame rate in the Output Module settings?
What is the codec in the output module settings?
Is your computer capable of playing back the final clip? Maybe it was compressed out of AE using the Animation codec, which would play badly on many computers.