How protected are the [FAT] partitions from viruses/malware?

Someone in the Operating System section of this forum told me to make this topic here in the Spyware/Virus section since it pertained to viruses.

After a recent infection of the AntivirusPro10 malware, I was forced to reformat my Dell Dimension 3000 computer to rid myself of the infection. During the XP reinstall, when the partition list menu appeared it showed 3 partitions:

-: Partition 1 [FAT] - 31mb (24 mb free)

C: Partition 2 [NTFS] - 72,635mb (65,173 free)

E: Partition 3 [FAT32] - 3.6gb (367mb free)

Unpartitioned Space - 8mb

I deleted the C: partition during the reformat because I knew that was where  the old infected files were stored. But I did not delete the two [FAT] partitions that were also listed because I didn't know what files were on them. Someone here at the Dell forum (in the Operating System section here) told me that those two partitions are where Dell stored the preinstalled WinXP OEM files (since my computer didn't come with any disks) and also some needed diagnostic files. The XP OEM disk Dell mailed me for the reinstall says on it "The software is already installed on your computer.". That is one reason I did not delete those two [FAT] partitions because I knew Dell preinstalled the OEM reformatting files on the computer, and I didn't want to make my computer inoperable or unrepairable by deleting files it needed for the reinstallation procedure.

What I wanted to ask was if anyone happens to know if the files stored on those two [FAT] partitions are protected from any sort of malware or viruses getting into them? I heard it somewhere on the internet that those hidden OEM reformatting files Dell installs at the factory are supposed to be protected from malware and viruses since they are not part of the working operating system and/or are hidden on the HDD, that only the files on the visible [NTFS] partitions are subject to malware and viruses. The malware installed a backdoor trojan on my computer and also ate up a lot of my system files when it struck, and I just want to make sure that it is 100% eradicated, and not possibly hiding in those two [FAT] partitions that I can't delete.

If I knew those two [FAT] partitions were safe to delete and wouldn't mess up my computer, I would just go ahead and do a second reformat and delete *all* the partitions during it to make sure the malware was completely gone. But from what the guy told me in my other thread I made over in the Operating System section in this forum, those two partitions are needed.

Thanks ahead of time for reading this. ^__^