What specific problems? I've used Banshee in MonoDevelop without problems. First of all, when you opened it, did you open the MonoDevelop solution file (Banshee.mds, IIRC)? Also, what are you using it for specifically? Just browsing the source, or building/running Banshee? Lastly, there is a lot of good general MonoDevelop documentation here:
http://www.monodevelop.com/Documentation.
Hope this helps,
Andrew