I am trying to install CentOS on a Poweredge 2900 and in the boot device menu the USB mounted is reading as the C drive. The problem I am running into is the drive I want to write the OS to is the HDD(s). I have removed one of the HDDs for another computer and I'm wondering if that has anything to do with the USB defaulting as the C drive or something else like that causing the failure.
You are trying to boot to the USB device to start the install correct? If you do that, install it and then take out the usb it should boot to the hard drives.
As Josh said, what you are seeing is completely normal and by design … once you install and boot to the OS on the HDD, then THAT will OS will report as the C: drive.