You can always use different threads in top and bottom, provided the tension balance is correct. You might want to experiment with Jamie Wallen's method of loosening bobbin thread as much as possible first, then adjusting top tension. This works with domestic machines as well as longarm, and works with any combination of threads. Some machines are finicky about what threads they like and don't like; experimentation typically results in threads that you want to use and some that you might want to skip. Here is a link to the Youtube video:
http://www.youtube.com/watch?v=Q1mRhcquZTM