I have recently been offered access to a couple of different pieces of encoding software (Cinema Craft, TMPNEnc.) and I'm trying to find out if these might be better alternatives to Encore in terms of overall picture quality and encoding speed. Cinema Craft in particular seems to be a very high end product.
And, if so, what will the process be to import these "already encoded" assets into my Encore project?
Cinemacraft will give you probably the best encode. Definitely better than using Encore to do it. Cinemacraft uses multiple pass encoding so the more passes you make over each frame, the better the image quality. It's like scanning a photo, one pass doesn't look as good as two. It takes forever to encode this way, but it's worth it. Usually it's about 6-10hrs for a 2hr video doing 6 passes (you can do up to 99) and 4Mb CBR.