I just have simple transition cuts to the next clips but it’s doing it’s on thing trying to fade them quickly or cross-fade them when I enhance. Is there any way for it to just leave them alone or do I need to enhance all the clips and relink prior to export in FCP?
You can either process each video clip indivdually or produce the whole final video and process it after. It depends on your personal taste. 
If you decide processing it after , I advise you exporting the TVAI process as Lossless compression (FFV1).
The problem with processing after is creating a blurred effect in the transitions.
Are you interpolating it?
