I've had no problem importing BIAB-generated midifiles into Encore and Sibelius scoring programs. The importation creates a score with each BIAB part on a separate staff.

Initially, after creating the BIAB file and saving it as a midifile, I open the midifile in a sequencer (I use Sonar) and delete the BIAB parts in which I'm not interested, usually leaving only the melody and harmony parts. Then I save the midifile, writing over the original.

Then I open the midifile in my scoring program and save it. Then I delete all the parts except the one I want to edit. After transposing or whatever, I print it out and save it as a separate file, like ROCKGLORY-baritone. Then I reopen the original and remove all the parts except the next one I want to edit.

If the harmony parts were generated by BIAB's harmony feature, I usually tweak the harmony parts, usually chord notes, to 'humanize' them since BIAB doesn't generate passing tone harmony unless the chord changes permit.

Editing the parts in a scoring program also enables adding of dynamic and accent markings, section markings, and comments, not practical in BIAB.