Mattresses are mekabel tumah. This means that if you find a blood stain on them greater than a certain size (a gris), it could make you niddah. However, currently, in the absence of the Temple, we do not observe ritual tumah and taharah in sense of there being any difference whether the bed, table, dishes, etc. are tahor or tamei.
Concerning not sleeping in each other's beds during a time of separation, "renaming" the beds by permanently changing their positions, bedding, etc., should be enough. If there are other aspects you are worried about, please get back to us and clarify them.