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 HD to this.
Going into the Advanced panel, into the QuickTime tab and choosing video settings, we setup iShowU to use the Apple Intermediate codec, at 30fps.

I then go to the capture options (the first panel, with the icon of a monitor on it) in iShowU HD and make sure that the Variable length frame durations is turned off. This takes care of the frame durations and makes them the same.

Turning Variable length frames off: If you don't do this, while the video might import into FCP OK - you'll likely find audio/video going out of sync over time.
Over in the QuickTime panel you can setup the video size. In this case, 720x400.

This one's easy enough - again in the QuickTime panel, check that the audio is setup for PCM 48khz.

With that done, after dragging the media into an FCP project, you should see the timeline like this:

The grey lines in the timeline area indicate that FCP can "RT extreme" this video. If either of these were red it would indicate that realtime playback after editing wouldn't be available (which is going to slow down your edit workflow).