I need to replace my alternator cover but I'm not sure how much oil will come out when I crack it open. Should I just drain the oil first or will I just lose a small amount?

You will lose almost no oil if the bike is up on the centerstand.

Same goes for the clutch cover. :)

Thanks mang. I was impatient so I got out the oil bucket and took it off. I only lost a few drops. Now should use locktite anywhere? The manual didn't say to use it though its generally a good idea of stuff like this. Also is blue rtv sealant the right stuff to use with the gasket? The manual just says sealant so I guess it doesnt matter.

I used a dab of black RTV on the crankcase seams, and where the stator wires come out, but that's it.

Just torque to spec (108 lb/in, IIRC), and don't worry about Loctite. :)