1. There's no such thing as "the NES emulator." Tell us which emulator you are using and maybe we can help you out. the answer is most likely going to be "you can't" though. I mean if you use MESS sure, but consoles aren't arcade games so I can't think of any reason why a console emulator would support displaying artwork.
2. You can probably use it, it just may or may not reflect your actual mapping and you might have to do more work. Most control panel display apps read mame's cfg files to compensate for any custom mappings you've made. With that being said you might be referring to navigating through the program. Something like joy2key should fix that problem. Btw they aren't keyboard emulators... they are keyboard encoders. An emulator would denote faking a keyboard, when in reality the hardware used in our hobby IS a keyboard... at least in terms of windows HID interface.