Usually FCP is decently smart about converting between interlaced formats. I assume what's going on is you're starting in 1080i, and because of a downscale, your interlaced lines are merging, thus you're getting painful flickering bars throughout your motion?
My suggestion is to maintain it as 1080i throughout your entire workflow, then dump a final file (still in 1080i) back into FCP. Doing a direct quicktime conversion to NTSC DV (or if you want, some other format; you can use that preset as a template at least, if you want some other color sampling or if you want top field first interlacing) should do the job, but please elaborate on your workflow if this isn't working...