There is a *lot* of firmware for serverboard S5000VSA. The best advice I can give you is this:
1) search support.intel.com for S5000VSA
2) filter search by firmware in far right category
3) sort results by latest by pressing "status"
4) download the Firmware update package for DOS (unless you have the Intel Deployment Assistant CD)
(here is where you decide which hardware you have)
5) download all the relevent firmware packages, if you have the hardware it's for, get it.
6) read the release notes from all the packages to decide on what order to flash the various firmwares in
7) carry out flashing firmwares following discoveries of step 6
I'm sorry I can't be more specific, but there are some things that I wont know since I don't have your server on my bench.