I'm not really sure what breed feeder mice are. They're usually indiscriminately bred so they could be a mixture. Probably the best thing to use in the bottom of their cage is Carefresh. Anything like newspaper or puppy pads they will shred, and I'm thinking the plastic on the puppy pads and the ink on the newspaper would be bad for them... They love to shred things. You can put some toilet paper or paper towel in there for them to use as bedding in their houses. Carefresh is best because they like to dig and it's better for their delicate respiratory systems, as well as for your allergies if you have them. Yes, males stink more than females... You are sure you have two males right? Just because the pet store says they are doesn't mean anything. That's how I ended up with 25. I use Nature's Miracle spray to clean out all of my pet cages. Unfortunately feeder mice don't normally live as long as other mice because they were bred for one purpose- food. Longeivity wasn't taken into consideration. I have one of the babies my mouse had still and she's about a year and a half.
As far as any addition information, make sure you thoroughly clean their cage often. They like to urinate on their wheels and houses so I normally put some bleach water in the sink and let them soak while I'm working on the rest of their cage. What type of cage do you have them in? If they start fighting, seperate them because they could fight to the death... This I also found out the hard way. The food that you feed them should be no less than 50% lab block and no more than 50% seeds and stuff. I buy Nutriphase mouse food and pet blocks from Petsmart (I know- evil) and mix it 50/50. Mazuri is also a good food I believe. I feed it to my hamsters and am happy with it but I don't know about the mouse formula.
Hope this helps. Good luck, and if you have any further questions, let me know.