Remove the Raid card. There should be three screws holding it place. Just take them out, replace the battery.
+
Remove the Raid card. There should be three screws holding it place. Just take them out, replace the battery. Here's a PDF from Apple on how to do it: https://manuals.info.apple.com/MANUALS/0/MA924/en_US/Mac_Pro_Early2009_RAID_Card_and_Battery_DIY.pdf