The most important thing is matching the iShowU settings to the FCP project settings. FCP will complain (in a number of ways) if these settings don't match. The important attributes are:
If any of these settings in the video differ from the FCP project, FCP will likely complain with General Error, error messages about the video not being optimized. In addition, if the settings aren't right then you won't be able to preview your edits in place without first rendering (say hello to a workflow that takes 10x the amount of time).
First, examine the Final Cut sequence settings.
Here's what's important:

So we have:
We need to match the output settings of iShowU to this. The reason being that we don't want the video to be scaled when we bring it into FCP. There's nothing stopping you using different video size settings, but you'll eventually need to rescale the video before bringing into FCP (see the section below on Recompression).
Final Cut is very particular about the video imported into a sequence. It must match (as you've probably figured out by now!) else you get warnings or worse the dreaded "General Error". Even worse is that it must use what we call "fixed duration frames" else it *appears* to work, but then doesn't. Here's a quote from a user summing up the situation:
"I have been using iShowU to capture sequences of images to edit in FCP. I am finding that I can edit the footage OK but when it plays back it will playback a different bit of the footage to the part I've selected. The same thing happens when I export the section of footage to try and lock down the frames I want, they come out as different frames. It has made for some interesting edits but obviously is not really satisfactory due to the random factor... "
Indeed!
To import footage from iShowU v1 into FCP, you first must recompress it so that it has fixed frame durations. Any recompressor will do. Stomp or QuickTime are are fine. Normally we'd not recommend this because it could lower quality, but there's no way around it for iShowU v1 footage - you must recompress it before bringing it into FCP.
In this case, we're suggesting you use either Apple Animation or Apple Intermediate Codec. Compressing twice using these codecs will result in next to zero quality loss (it's also reasonably fast). Next we take you through recompressing using QuickTime 7 Pro (QuickTime X doesn't provide any recompression facilities as yet).
Here's a quick video showing how I exported a movie using the above settings, using QuickTime 7 Pro. The important things to notice are setting the correct codec, and selecting PCM 48k for the audio.