Sibelius may automatically group beats appropriately for each time signature you create, but maybe you had a pick-up note(s) at the start of the jig. If so, type in rests before the pick-up notes so the first measure is filled up. Then see if the software doesn't put the beams in automatically.

Check to see how the B part begins, as well. The software needs to see 6 eighth-notes' worth of music in every measure to do the automatic beam. After it's done that, you can remove the rests, tidy up the repeat signs and save the file.

That's what happens in Noteworthy, anyway.