You're probably suffering from the "Windows USB device remapping" problem
Mame refers to USB devices specifically by their enumeration order, so if you install other devices, they can all shift around, when means Mame won't refer to the proper devices anymore, and you'll have to reconfigure.
If you install all your devices, then config mame and never add or remove (or relocate) devices, that's all you need to do.
If you plan on pluging and unplugging devices often, though, you might want to take a look at my ControllerRemap utility (the link is in my sig). It allows you to setup the mame config file such that things can be remapped properly when you start mame, no matter where the devices currently enumerate.