I've always had the best luck with crate training. The thing about training two at a time, is if one has an accident, the other thinks it's "okay" to have an accident there, too -- but you can't very well punish the pup that didn't have the accident for what the other did, and what he may do later. You just have to be twice as vigilant as you would with one puppy in the house, which can be a total pain in the ass.

The puppies we have now have been crated at night on a bed of cedar, and an advantage to this that I didn't think of before is that they're almost "litter trained" now -- that is, they won't generally use the bathroom unless it smells of cedar where they're going. So, even when they're running amok, if they have the urge, they'll stop and sniff their way back to the crate to use the bathroom, we change the cedar, no mess no fuss.