There is a very good chance the other one is in the HVAC system or vents somewhere. Possibly the fan assembly.
A past Subaru Legacy and Chevy Metro had mouse nests in the HVAC squirrel cage fan. There's irony for you.
Also bad is that the little @#$% probably left droppings in the HVAC system as well. Can you say "Junta Virus"?
A good strong vacuum at the floor ducts might be able to pull out a carcass and droppings. For the fan, you will have to remove it.
Mice can get in by climbing from the inside of the wheel up the suspension in to the engine bay, and from there, up to the top of the firewall, over, and into the HVAC intake plenum. The lip of the plenum is raised, so to prevent rain water from flooding in. But the dumb mice climb over the lip, fall a little over a foot to the fan assembly and then work their way through the blades and into the HVAC system.
If you have a cabin air filter, they would have had to chew through that. Check it for holes/tearing. If you got holes, thats how the little @#$% got in.
Auto part stores might have an aerosol disinfectant to de-germ the HVAC system. Lysol perhaps?