to pick the extruder just click on the object and go to the bottom option on the left hand side of the screen.
You can choose which extruder to use from there (can't currently remember what it's called).
At the moment I just use the left extruder as the right nozzle got blocked and I haven't put it back yet.

Also if you make a custom profile - be aware that makerware ignores all current settings resest everything. So don't assume that the settings you've just set will carry through to nthe custom profile - they won't. I've found them to be more hassle than they're worth. Also you can't load a custom profile and then tweak quality/speed or temps. That's just stupid right there.

ALso if you switch from direct print to export to sd - it changes the speed settings, so check them again.
It's stupid little things like this, that stop it being a great piece of software.

That said I've never felt any real need to mess with anything but the standard: temps/quality/speed. I'd like to change first layer settings but couldn't figure out how even with proftweak.

So until i can use a different piece of software - makerware does the job and for the most part, does it quite well.