Easy way I think would be to run windows xp setup and format the partition you want to format.
to format a partition safely, LABEL your partitions if more than one, so you know which is which. And you can remove any hard drives with partitions you don't want to format.
You can format from windows xp setup cd. (important to have one anyway if you have windows xp installed!)
A less easy way, would be to make the other windows partition active, the C and D will then be the other way around. You'll want to format D. And you can do that by booting off C and starting windows from C.
Here is some terminology that may be of interest to you
difference between system volume and boot volume
(though terminology seems a bit counter-intuitive to me, and I don't really use it, system volume starts first, then the boot volume.. and with that termonology i guess it looks like 3 volumes.. a system volume and boot volume, (C), and a boot volume D)
i'll use the word start instead of boot, so as to avoid confusion with that MS terminology.. the active partition with boot.ini that one starts first and is C.
The other partitions it sees with windows on them, are later letters.
Make any one of those other partitions the Active one (give them the boot.ini and other few files..), and that partition will then be C.