to generate for just part of a track use the 'from' and 'to' fields. i use multiriffs to generate solos in songs - say a verse as an instrumental break.

its quite easy to deal with a shorter section than a complete track. the program looks after making it sound good starting and ending rather than have phrases overlap and not finish properly.

when the multiriffs are generated, audition each one separately - the program will play the section of the song where you want the riff and the chosen riff itself and you can see how each 'fits'. you might like one or more version. you can choose several and edit them together - intro from one, ending from another etc later when you've imported them into separate tracks.

that's how I work. just be careful - when you are auditioning riffs don't hit the ok button which is a little too natural for my liking - you'll select the last riff you played and insert it without listening to the others! only hit ok when you've chosen the riff or riffs you want.