It depends on the game, there is no general rule that matches all games... http://www.realmodscene.com/index.php?/topic/5040-multi-disc-again/ in this thread i explain it, hopefully in a good way...
Basically, you can extract both discs and look for a "Content" folder, if there is one on there, then it's likely something you need to "install", that disc is generally also the multiplayer disc, or just a installation disc... so, you can most of the time discard it once you've installed that data, unless you want to play on LiNK (and it's supported, not all games do support LiNK)
Adventure games tend to be continue playing on the next disc, so those are generally ISO2GOD all discs... but, that's not always the case...
Bottom line, look around, there's bound to be someone that explained every single game that have special case operations, if there is no special things required for the game, just go with whatever you prefer... (not finding anything is generally a indicator of that, however it depends on how recent the game is, sometimes there are games that need special treatment that has just been released and nobody has posted how to do it for that particular game yet)