Most of the oil should be in the sump, so you shouldn't have to drain the oil.
There will a small amount of oil behind the cover, but it won't be a lot.
The gasket sealant goes on the alternator cover surface and the grommet for the alternator cable.
Apply a light thin film of sealant on the surface with the dowels out and allow to set for a few seconds. Then insert the dowels and overlay the gasket.
Then attach the cover, insert the bolts, and evenly tighten to spec.
I use Yamabond, but the other gasket sealers are pretty much the same stuff.