I have Drive C: and Drive D: but my Drive D: only has 2 GB's of space and everytime i want to install something, it automatically install's into Drive D: where it has no more room left. There are programs that allow me to configure the installation to Drive C: but for some programs it wont...is there a way to make everything download to Drive C: ?

i dunno try assigning drive C with the letter D and assign drive D with the letter C

the installer should have an option on where you want to install the program
example:
one of the installer step will say it will save to this directory eg."C:/program files/program". somewhere near it it should say change directory or you can type in the directory yourself (on the "C:/program files/program" text field) (im not saying every installer will have this. This is just an example of some installer will have)

Is it two actual hard drives or one partitioned drive? I'd always use the smaller to hold the OS and main system files. And the larger for extras. Make sure when you install you always select the custom or advanced installation type that way you can always choose the installation directory.