Wire both controls separately.
Most games that were released with cocktail flipping (all the popular ones like Pac-man, Dig Dug, Centipede, etc) also support it in MAME (but no all). These games should automatically use the default MAME controls for player 2 when put into flipping mode.
I don't know of any games with flipping that don't use the player 2 controls properly (except ones that come with the warning about not supporting flipping), but I wouldn't be surprised if there were some. If you have that problem, just set your IPAC to reprogram every time you start and exit that game; you'll set the player 2 controls to the same config as player 1, then reprogram them back to normal when the game exits. There's a couple ways to do this, but I think the easiest with with a batch file. The IPAC utility can be ran from DOS by feeding it the name of the config file you want. Then run the game using the MAME command line function. The batch file will freeze while the game is running. When you exit the game the batch file will resume and you can reprogram the controls back.
Here's an example batch file (though you wouldn't use this for Star Fire):
cd\
cd "program files"
cd "winIPAC"
WinIPAC.exe c:\program files\winipac\allp1.ipc
cd\
cd "MAM32"
MAME32.exe c:\MAME32\ROMS\starfire.zip
cd\
cd "program files"
cd "winIPAC"
WinIPAC.exe c:\program files\winipac\defult.ipc
The above also works great if you are trying to play old PC games on your arcade (like old PC versions of arcade games) that don't allow you to reassign the controls. Just copy the text into a new text file, change the parameters, save and then rename to whatever.bat