I've seen it done both ways. Whether using one goalie or having alternating goalies is better depends on the goalie(s) and possibly on the coach.
During UMaine's first national championship season, Walsh alternated between Mike Dunham and Garth Snow (both now in the NHL) and they thrived.  The benefit of having both goalies--and goalies with different styles--available was demonstrated in dramatic fashion in the 1993 championship game, when Walsh pulled Dunham after two periods and inserted Snow, who was a much better puck handler.  Snow acted line a third defenseman, clearing the puck and allowing Maine's forwards to go on offense.  Paul Kariya set up Jim Montgomery for three third period goals, and Maine beat Lake Superior, 5-4.  By contrast, in the last three years, including Maine's second national championship in 1999, Walsh wound up going with one goalie--Alfie Michaud in 99 and Matt Yeats in 00 and 01.  During the last two of those years, Walsh started by alternating Mike Morrison and Yeats, but Yeats came on strong in the second half of the season and became the No. 1 goalie.  Given Maine's final four and final eight seasons, I'd say that work
ed, too.

I'm not sure what Tim Whitehead will wind up doing this year.  So far, he's indicated that he'd like to alternate Morrison and Yeats, but I think that will depend on how the two of them perform.  We'll see.