Make sure both pads are recognised separately, before running an emulator
You can use something like Joy2keys
http://joytokey.net/en/ and test in notepad just setup one pad to start with (while both are plugged in and operating) and make sure Pad 1 is working with the keys you binded, then test Pad 2 and make sure it does not produce the bindings from Pad 1
If they both end up using the same bindings then both pads are using the same output ID, that would explain why it is seeing both pads as Pad1 even though you setup player 2
If they Pad 2 does nothing when Pad 1 has keys binded while Pad 2 has no bindings, then bind different keys to Pad2 then do some more Notepad testing
If all goes well and both pads have different keys binded then you can use a NES emulator setup to keys for both players as the Pads when bined with Joy2keys will act like you are using a keyboard, just without the limit of only being able to use 3 or 4 keys at once whatever the keyboard limit normally is does not apply to keys setup via joy2keys to a control pad or more
You can either have one pad binding to keys or both just as long as they work independent of each other