It's risky, since the match engine isn't at it's finest when interpreting three at the back, but it's possible to make successful. Few quick tips, though:
1) Against teams playing two players upfront, flat three is a decent way to go. (3 v 2 at the back)
2) Against teams playing with a lone front man, use a libero with attacking duty. It's not beneficial to have three CB's at the back marking one striker while going forward.
3) A good libero / sweeper is the best way to go, though it might prove to be expensive. Then you have pretty much the ideal setting, using a sweeper behind two man markers when facing a two-striker system and switching to libero when against a lone-stiker system. Then you'll always have an extra man at the back without sacrificing too much attacking potential.
4) There are few tricky shapes you might encounter, a three striker system (eg. 3-4-3) or 1-2 at the front (eg- 4-3-1-2). There are shapes to counter these formations (eg. 3-1-4-2 / 3-1-4-1-1 against 4-3-1-2 - yet preserving that extra man at the back), but the match engine isn't too fond of these formations, or you might not have the players to do it and it's also quite rare occurrence. So a good way to work around it, is switch to far less aggressive pressing (in case you play with higher setting as default), so you won't get dragged all over the place and the team concentrates on keeping the shape intact.
Best of luck!