yeah always take your liners out, they get wetalso look and see if water is leaking through the toes in your shells, it happened with my boots and i put some duct tape on the inside to seal the hole and they don't get wet/smelly anymore
if you have a boot dryer put dryer sheets over the part where the air comes out. and if you dont have a boot dryer just put dryer sheets in after you use them. it works really well
or, you can choose to be an ass like me and let the smell build up and then sell them at a swap someplace. but that is pretty mean.
i pull the liners out and put some boot dryers in them but they still smell, which sucks for me.