Your transmission has input shaft bearings, output shaft bearings, and roller bearings. As far as I know, no manual transmission has a "main" bearing.

Just keep in mind that whether it's a bad transmission, or a bad throwout bearing... that it's EXACTLY the same amount of work to diaggnose or repair.
To a mechanic that spends every day fixing other people's crap, replacing a transmission is a much better paying job than replacing a $15 throwout bearing.

I've seen a rash of clutch problems mis-diagnosed as tranmission problems lately. If it makes a grinding, hissing, or squealing noise when you press the clutch in... new clutch bearings or not... it's probably the throwout bearing. Especially if there's nothing wrong with your fluids. Definitely get a second opinion.