sega joystick help

[langdoguk]

Hi there I've just added sega megadrive games to my cab but I'm having trouble with the controls ,the 'up ,down ,left +right ' with the joystick works okay but its the jump , hit button etc . With some games player 2 buttons work with joystick 1 , some other games joystick 2 left is jump etc. I'm using Atomic FE with an Ipac 2 (I've never had to keymap etc , it worked right out of the box for mame for me). Is there an EASY way to set the right buttons for the right joystick ?
I thought there might be problems but thought I would give it a try , any help would be great , thanks Craig 

[SavannahLion]

Are you using the same emulator for all of the genesis games?

[langdoguk]

I'm using Atomic FE plug & play module for them , I tried going to the Fusion.exe file in plugnplaymegadrive and define the controls , but I've got a new problem now , I don't get a picture now after I changed them , I can hear the game but have just a blank screen , not sure what I've done ??