Once you get them spayed or neutered, I would recommend watching some YouTube videos called 'Howcast' on how to deal with an aggressive rabbits etc (not that I am saying you are a bad owner because I have never seen you do if before) because I have learnt a lot from it all.
I agree, I use wood shavings all of the time with a thick layer of newspaper underneath - however I place it there so that the urine doesn't ruin my hutch if it ever gets too wet. Also I heard that putting hay where they do their business helps reduce the smell. Not sure if it works but worth a try!