Don’t mess with the GOP settings unless you know EXACTLY what you are doing.
I use 2-Pass VBR when I have the time and/or when it’s challenging and highly varied content.
If you need to archive your content as well as use in FCP I’d choose either Animation or PNG. If it’s just for use in FCP and you are compositing it with video content then render to the same codec as the content you are mixing it with.
Adobe announced a while back that Encore will be available on the Mac pretty soon probably launched at NAB in April. I’m not sure if it’s gong to be available seperatley or only as part of the Adobe Production studio.