Neutering/spaying is actually a good way. Smelly rabbit poop (assuming they are healthy) are usually the territorial poop, which is coated in kind of a sheen, oil. Non-territorial poop looks identical, but it's completely dry and doesn't smell.
Spaying/neutering helps reduce the need to mark, so those more smelly poops may reduce.
Aside from that, cleaning the bathroom area regularly and keeping all surfaces dry will prevent smelly bacteria from growing!