You can choose the main program folder in the D: , but there are some common files of the software, which are generally located in System Drive:\Documents and Settings\User\Application Data\
These files will remain on the system Drive, and you cannot move them to D: .
You should not install programs in the other drive, rather, move files like songs, videos, other large files to the other partition.
I say this, because, after a while, both your drives will get cluttered with programs, and it will be very difficult to manage them. You will end up installing the same program in both the drives, thus resulting in more space wastage.
Though, technically, it is absolutely not a problem/issue in installing to a different drive, I would not recommend it. I have installed a few programs of mine in the other partition, and I sometimes regret doing that, for a simple reason, that I wanted to format the other partition, but because my software was on that, I could not do so.
Keep these little things in mind, and proceed