They're both great programs, and there's no reason you can't run both on the same league. They both add a lot of enjoyment to the game.
Installing BOSI locally is a bit daunting though (you essentially need to set up a server). It's mostly geared towards online leagues, but has some neat features for the solo league as well. You can track rating and talent changes as they occur, for individual players or teams. You get stat breakdowns by position in the batting order. Those are really the two things I find most interesting out of BOSI for the solo player.
You run Cato at the end of each season, and it creates a baseball-reference style report. It will output very detailed information on lineups, statistics, awards, etc. Cato has an example of the output at his page I believe (
www.jcato.net).