Yes, you should boot into DOS, with a boot disk made from just about any Windows OS, run fdisk and format beforehand, right after you build your system and before you install your operating system(s). Fdisk and format is partitioning software, and it's just about everywhere nowadays. If you need help with it, Radified has a guide for it, just click the link below and look around for it. I would reccomend printing it out if you don't have another system handy.
How big is your hard drive? If it's big than you should follow
Radified's Partitioning Guide, as I did. It is very useful and can help maximize the performance of your drive.
Typically I go for an 8GB system (OS), <2GB swap partition, then build up from there. Using this strategy, an extra swap partition, all but eliminates the need for fragmentation which is pervasive with single partitions. You can find out more about fragmentation in the Storage and Networking section, where there is a sticky thread explaining it.
I would reccomend using FAT32 for most of your partitions, and NTFS for large partitions that either are too big for FAT32 or are going to be filled to the brim with data. My 43.8GB G: drive is NTFS, and it's compressed, but it still only has almost 8GB free.
My other drive, 10GB, has an 8GB and 2GB partition. It's Red Hat 8.0.
If the attached file doesn't work, click the link in my sig and scroll down to my partitioning section. It has a picture with my partitioning strategy on it. The Images partition is for Norton Ghost images of my sys partition, not pictures.