I would ignore the message for the time being. Yes, there is a chance, if it has been left unplugged, that you will need to replace the battery, but it also may just need to charge. Boot to CTRL-R and configure the drives in a RAID array, initialize, and let it sit for a day or so (it will not charge if there is no configuration).
You can update the BIOS without an OS, but it is much harder - and it will probably not help (it is the RAID controller that is responsible for the charge of the battery, not the BIOS/system).
The no hard drives could be either 1) RAID is not configured (the PERC controllers do NOT support non-RAID, so all drives must be configured before the OS can see them), or 2) you did not load the drivers for the controller.
If I may give you some advice ... unless you have a really good reason for learning how to work with, manage, install 2003, skip it. You can download a 180-day evaluation of Server 2012 to install on it.