If I'm reading this correctly, it sounds like you've got it set to "mirror" your MacBook display (replicate it on the larger, connected LCD) rather than spanning/extending your desktop?
I don't run this type of set-up, but I've fiddled with it in stores before. I can't remember the
exact thing you do, but I do know that you go to the Displays preference panel in your System Preferences, and there should be something there that lets you toggle from mirror to spanning.
Someone else can probably get a bit more detailed about it, but it sounds like you just need to click a button or two in OS X (assuming I'm understanding your problem correctly).
EDIT: chucker got it...nevermind.
