Bowman seems more like a classic 4-3 LB, strong all around, but not a terribly gifted pass rusher. Kind of like Manny. Hard to see two guys like that playing together in a 3-4. So, I'm thinking he backs up Manny, while the three-headed monster of Haralson, LaBoy and Brooks man the other side.
The other possibility is that the Niners want to trade Manny and see Bowman as his replacement. I think this would be a mistake. Manny is a terrific all-around player. He's fantastic in coverage against opposing tight ends, for example. And he actually led the team in sacks last season. So I hope they keep Manny and just use Bowman as his backup.