Just like in the physical world, there can't be more than one music distributor bringing the same album to the same store. Otherwise, when the album sells, how would the store know which distributor to pay?
CD Baby will never prevent you from doing anything you want with your music. For YOUR sake, though, please note: If you sign two digital distribution deals with two companies that will both be sending the same album to iTunes, Amazon, etc. - this will hurt you, because the retailer will usually remove the album from their store completely until you decide which distributor has the exclusive right to be selling the album through them.
If your distributor offers distribution to a partner that CD Baby does NOT have a relationship with, then it is perfectly acceptable to use their distribution services for that one partner - and then use CD Baby to distribute to everyone else.