You might not be able to do it in 2010 since it had the HST changeover tool in this version. I am not sure if you mean you have 3 companies in 1 company file or 3 different company files with 3 classes.
I have used Quicksbooks for quite a few years now and prefer it over the others. I personally have not experieced any of the glitches as I think I heard the most about 2008 having the most bugs, however my transition from 2007 to 2008 for my clients went very smooth. I will being updating to 2009 in the next and look forward to the new features. Will let you know if I have any problems.