@Sandy27, I have the same situation - 2 rooms + bathroom.
Though I've decided in the meantime simply to rent out one room, my only option was (as @Marit-Anne0 suggests) to list the rooms separately. You could copy/paste one room's link into the other room's listing, and emphasise in your description - also in the listing's heading under the main photo -that both rooms are available/intended for a party of three.
Emphasising that the accommodation is geared towards three-person parties might help prevent situations where two people book, but decide to split the sleeping arrangements, leaving you with two lots of bedding to launder. Though in case of a two-party booking, you could leave the unbooked single room closed (or locked if it has a key) and the bed unmade (with only a coverlet on it for appearances).
(I don't recall offhand whether the accommodation options include 'suite', but this might be a way to go as well.)