With a Perc battery replacement it is simply powering the server down and then swap out the battery. You can then leave the server off, yet plugged in, to start putting a charge on the battery. Power the server up and everything should be done. Now if you plan on replacing the perc dimm there is a procedure to adhere to in order to protect the dimm, but the battery not so much.
Let me know if this helps.
"You can then leave the server off, yet plugged in, to start putting a charge on the battery."
Just to note .. you don't have to leave it off but plugged in. If you do, then when you power up the system the controller cache should be enabled, but if you power it on immediately, the controller will disable the cache until the battery has sufficient charge to enable it - this will be done automatically and on the fly. There is no need to worry about cache contents AS LONG AS the system was shutdown safely and gracefully.