Defragment the C: drive; fragmentation may slow the drive down if it doesn't have a lot of free space (this is much more true if you have it formatted as FAT than if you have it formatted as NTFS). The defragmentation gadget (right-click on the drive in Explorer, then Properties | Tools | Defragment Now) will tell you if defragmentation is really needed or not. This built-in defragmentation tool is not the fastest or the fanciest, but it's safe.
Do not put programs on one drive and data on the other. If the drives were two physically independent disks, that would be a good idea, but when they are actually the same physical disk, it's a bad idea, as it will hugely increase access times. You can put programs with their data on the second drive, but don't put a program on C: with its data on D:. Data that isn't constantly accessed (such as a Word document) can be put on D:, but databases and the like must stay on the same drive as their programs when both drives are physically one.
A slowdown on the machine, if it hasn't been slow before, could be fragmentation ... or it could be malware infection.