Just my two cents...
If the program/game isn't specific on which drive it wants the 2nd disc to be in, you are in luck. An image mounting app, such as Alcohol 120% or Daemon Tools Lite will allow you to mount multiple images (.iso, .bin, etc) to seperate 'virtual drives'. As far as your computer is concerned, these drives act just like a physical cd/dvd-rom.
If however the game expects the disc to be in the same drive as the first, you're out-of-luck. (You could at least alt-tab out, unmount the first disc, mount the 2nd disc, and try that)