@xyphoid:
You first have to assign keys to buttons via Poseidon, then, within FPSE GUI, configure joykey.dll simply pressing desired button on the pad when asked to (i.e. press "Change" and then the button).
If your controllers are already configured for mame (in Poseidon I assume), you should have no problems.
I have one key mapping for pad1 and one for pad2 and I use them in mame, FPSE, snes9x and so on...

If that's not the case, maybe I didn't get the point.

@Condor:
I guess your problem is the opposite: you can't map keys to buttons, isn't it?
The hardest part in Poseidon config is guessing how X and Y axis work: there is a sort of threshold when the directional pad is in "rest" position and a max value when it's pushed all the way in a direction and a min one when its pushed at its opposite.
For the buttons, you have to set a keypress event and a release event, otherwise the mapped key will always result pressed.
I swear I don't speak a single french word, but I managed to figure it out following the guide I posted

With a little help from Google, that is...

Hope I helped somehow,
M.