I have multiple monitors (three to be exact) and whenever I try to run the program it always shows up in the left monitor instead of the center (main) monitor. Then whenever I try to click on anything in the game (like the new game button) the program goes out of focus as if I had clicked somewhere outside the game screen. I can't really seem to find a solution to this myself but does anyone know a solution?

Except I can't do that! When I try to click on the options button in the menu it leaves the program like I mentioned, or is he talking about choosing a hardware device somewhere in the actual game files?

try running windowed (see the sticky/useful links), that should allow you to modify the video options. by default, the game should pick the primary monitor.