Not a problem!

It was still raining when Noah got them animals on board and floated off. It would have taken 'awhile' to "cover the entire Earth"...maybe for...ummmm.. 20 days? Then 20 days to recede and drain back into those convenient underground chambers. (which, I assume, God closed for those 20 days to allow the flood to progress.) Perhaps it continued to rain off & on, even as the flood was receding.... (and of course, the two camels had plenty stored)

It's easy, if you just start with the assumption that it DID all happen, and that God could arrange it anyway he wished.