@1: I would import samples which already contain modulations. You can still add more on top. Several layers of modulations sound nice, at least in my opinion.

@2: Having read your last paragraph, I would say that you don’t even need resampling for transitions. Play with your Jomox, build OT/synth stuff on top, reduce synth stuff, change pattern/bank etc. on the OT while the Jomox is in focus again. That’s how I do it with my MD+A4 live setup, very basic, very straight-forward procedure.