I know that in FCP 6, when you drop a clip into a new sequence, it will ask you if you want to match the timelines settings with the clip when it’s the first one dropped into the timeline and the settings don’t already match. If your version doesn’t do that, I would recommend downloading the free MPEG Streamclip and use that to batch convert your original media to whatever the codec of your timeline inside of FCP is.
Posted from iPad, please excuse typos!
Tony Brittan
Island Shore Productions