Don't use Noteworthy... Making a multi-instrument piece just gets aggravating. Try Finale... It makes decent midis, though there are definately better programs out there.
Everybody hates Noteworthy, but I use it, and prefer it over anything else. But then again, I'm also a classically trained musician, and therefore it makes it easier for me. Finale is best used for making actual sheet music, and printing it out. While you can make MIDIs, and play them back, it isn't as customizable as Noteworthy.
*Hides from people who know Finale's capabilities while they throw bricks at him*
Ahem... let me explain.
Finale is a great program, and is worth the money... but if you're just wanting to make MIDIs, go with Noteworthy, or even still a different program. You have to learn how to use Noteworthy Composer before you can say it isn't any good. For making MIDIs, Noteworthy completely obliterates Finale. But, for making sheet music, Noteworthy doesn't hold a candle to Finale. Nobody seems to get this, they just immediately put down Noteworthy because it's complicated to use at first. But... what do I know? It's not like I compose music or anything...