I complained to Womble about their encoder and suggested if they couldn't improve it to at least allow external encoders. No luck there.

I finally settled on using VirtualDubMod (it can load mpeg files) for simple croping, filtering and resizing (I'm lazy) and frameserving to CCE.
For any crossfades or transitions I used avisynth and again took that to CCE.

Just make sure your framerates match. That is if your main movie still has 24 -> 30 pulldown flags make sure you add flags to your re-encoded clips before going back to Womble with them.