Re-using a clip

Can anyone help here? I am trying to overlay clips using Slick 4 Mattastic.I want to use different parts of clips as the overlay at different points. After using part of a clip for this I cannot reuse a different part of the clip further on over the base clip, it always seems to revert to the first edited part of the overlay clip even after restoring it and re-editng it. Paste over is not suitable as it can't be faded in and out and as the background clip is a piece of music simply cutting and inserting isn't what I want as the transitions will cut part of the sound track. This is easy in Final Cut where I first started this project but it makes a mess of some other media types which iMovie handles well hence reverting to iMovie. Exporting from FC via Quicktime Pro works but then has to be re-converted back to wide screen - very time consuming.
Any advice will be gratefully received.

You are taking a 720x486 clip, and blowing it up to 6 times the size, and trying to retain some semblance of quality...YES the MM will take 16 hours. It takes time to do this. Want to cut this time? Get an HD capture card and capture the footage via the card, upconverting it as you capture. Then the process is real time.
Top end machine or not, you are asking a lot, and it will take time. This isn't a 10 second or 2 minute clip...it is nearly an hour long.
Shane

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