iTunes not recognizing apps

[divabimbers]

Well, had to bring my iPhone to the app store since couldn't restore but now that it's home and working, I've ran into a bit of an issue. My iTunes library is stored on an external since it's too large to fit on the MBP but when I go and plug in the iPhone, it doesn't recognize all the apps I have. Instead, there's an exclamation mark next to them. Is there a way to get iTunes to locate all of the apps at once rather than my needing to go through them one by one and manually locate them? Also, could someone write out how Apple has the iTunes directory laid out since mine's a bit of a mess and maybe if I can get it organized the way Apple does it, I can get iTunes to track down the apps itself. Thanks!