The RAM is already cleared if the battery is dead. You probably won't have to do anything but put the new battery in, turn the jackpot reset key a couple of times when the RAM error message appears, push and hold the MPU self test button for 2 - 3 seconds when it tells you to and close the main door. Most of the machine settings are restored from the EEPROM on the backplane. Enhanced sound (if you have it) is one that you may have to change.
Normally the only reason to ever use a clear chip is if you want to make changes to the accounting denomination. The clear chip clears both the RAM and the EEPROM and then you have to set the machine up from defaults all over again. This normally causes a lot of problems for novice users so don't do it thinking it will clear an error. It won't, and will cause you more problems unless you know what you're doing.
The battery you're replacing is the coin cell battery right? If it has a green varta battery you should get rid of it before it leaks and damages the board. If you have a 500 series MPU you can just yank it out, if you have a 1270 you need to remove U16 as well.