So I think I solved some of my import issues. I did a test last edit last night using two episodes from Lost BR. I did my normal process of ripping these two episodes as .mkv then using HB to convert them to .m4v files (my end result is normally to have AppleTV compatible files which need to be .m4v or .mp4). I then used Mpeg Streamclip to convert these two new .m4v files (not FCP compatible) to .mp4 files. I was then able to import and edit the two epsiodes together (removing credits, and previously on footage, etc).

Now the issue I have is getting this newly merged and edit movie exported back to an .mp4 or .m4v that can be used with aTV. I am using FCP 6 so I only seem to have Export to Quicktime and Export to Quicktime Compressor as my export options. When I tried doing the Export Quicktime Conversion method, I end up with only a .mov file.

Does anyone have any ideas on this? How can I export to a normal .mp4 file?