Here's a great tutorial covering much of what you're asking by Walter Biscardi.
http://library.creativecow.net/articles/biscardi_walter/realtime_sequences....
When exporting from Streamclip, be sure to use a QT codec FCP likes such as DV or DVCPro 50 (might be overkill for Flip video). Do some tests on a short clip and see what works best for you. It's possible Compressor would work for the conversion, but I don't know for sure. I've never tried that.
John
MacPro 8-core 2.8GHz 8 GB RAM OS 10.5.5 QT7.5.5 Kona 3 Dual Cinema 23 ATI Radeon HD 3870, 24" TV-Logic Monitor
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Final Cut Studio 2 (up to date)
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