2 cats are apparently easy enough, as I mentioned before I've seen some inexpensive little doo-dads that are designed to replace the second pair of 02 sensors and deliver an "OK" signal. The OBD-II system apparently doesn't use the second set of sensors in any way other than as a potential flag that the main cats have failed, they are not involved in the closed-loop feedback.
Going down to 1 main cat would probably also be easy enough, the 02 sensors should stay far upstream, but the cat itself could be located further down. It really should be as close to the exhaust ports as possible so it can get to and maintain light-off temperature as easily as possible.