What you can do is change the active partition and then make sure your bootloader is correctly setup.
Change the partition that has your OS on it to active using fdisk or partition magic etc.
Now since you've changed your active partition to C: ( this is what I think you're trying to do), you may need to to change your boot.ini file. You can access this by typing-- edit c:\boot.ini --from the run command, or going into the control panel>system>advanced>startup&recovery>edit boot.ini in Windows XP.
Looks like this for NT, 2K, XP. Make sure the default=[points to the location of the operating system]
[boot loader]
timeout=3
default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows XP Professional" /fastdetect
Looks like this in 95, or Win 98
[boot loader]
timeout=3
default=c:\WINDOWS
[operating systems]
c:\WINDOWS="Microsoft Windows 98"
If your C: partition is set to active and your bootloader looks like one of the above you should have no problems. Your other partition can be used for program files and one for data.