from what i can remember from phpBB setup, you're asked what prefix you want the tables to have. by default, it's "phpbb_" yeah? so, just make your second board have a totally different prefix.
for clarification, let's say you're hosting a God board, and a Satan board. the easy thing to do would be to prefix them as such:
"god_" & "satan_"
there's not much chance of confusing them that way. as madra said though, server load will come into play too.