number one, in professional studios and such is if guitar recorded internally; as in through a line-out etc directly to a computer, or with a microphone recording the output of an amp?

and second question is, anybody know/have an opinion which effects board has better recording capabilities between the Boss ME-50, and the Line 6 POD 2.0?

For the first question it's either or, sometimes both. When I record I run through my effects board, through a mixer and then into a computer.

As for the second one I have no idea.