There's no simple answer, alot of what you need to do deals with your editing system. Try cross posting this in the FCP forum.
Before editing software improvements, you would have to correct it into the format you plan to export it to, in order to avoid problems. I believe FCP is strong enough to handel this on it's backend, but I work in premiere.
I'm by no means an expert when it comes to editing, but I believe you would do right in keeping the fcp sequence upper field. Since you have material in, and will be exporting to, animation codec, I'd say it makes most sense to use that as your sequence settings. But I may well have overlooked something, so do ask the folks in the fcp forum as well :-)
If your sequence is upper from the start, fcp should automatically add shift field filters to any lower field footage added into it (and vice versa), but if you change sequence settings after editing, you'll probably have to do that yourself and/or fix any now incorrect shift field filters. (Same thing goes for mixing footage with different aspect ratios in fcp, by the way.)