Thank you for your replies! I’m now in the process of converting my clips to Apple Intermediate Codec with MPEG Streamclip, which works great. When I import it into FCE I still don’t know which Codec to choose from in the list. Right now this is what the list of Codecs to choose from looks like (When choosing sequence settings).

The majority of them are either low quality or 1080i, but I’ve shot in 1080p, which seems problematic. Now that I’ve converted them though maybe that changed but I’m not sure.
I did however deselect the interlaced scaling option when i converted it, not sure what that makes the clips now.

Any ideas on what Codec to use now? All my footage is shot in 1080p.