How to upgrade bq78PL114RGZT to bq78PL114S12?

IMHO:

First you must read a few technical documents to get the necessary understanding on how a bq78PL114  based BMS system works.This is very important.

Then you know enough to be able to upgrade the firmware using bqWizard as described in the documentation.

Here is what you must read:

bq78PL114 and bq78PL114S12 Technical Reference Manual (Rev. B)  (PDF  352 KB) 
  25 May 2010  374 views  Read Abstract

Quick-Start Guide for BQ78PL114 with BQ76PL102 Family Gas Gauges  (PDF  4135 KB) 
  26 Apr 2010  215 views  Read Abstract

These documents will also soon become useful/necessary litterature:

PowerLAN Gateway Battery Management Controller with PowerPump Cell Balancing (Rev. B)  (PDF  574 KB) 
  30 Apr 2009

bq78PL114 System Design Guidelines  (PDF  9561 KB) 
  01 Dec 2009  281 views  Read Abstract

bq78PL116 Technical Reference Manual  (PDF  649 KB) 
  21 Feb 2011  271 views

bq78PL114 8S EVM (Rev. A)  (PDF  2281 KB) 
  14 Jan 2010  341 views  Read Abstract

Wide-Vin Battery-Charger Using SMBus MSP430 MCUs and bq Fuel Gauges  (Multiple Files) 
  08 Feb 2011  1,934 views  Read Abstract

Also be aware that the bq78PL114 has been replaced by bq78PL116 as the recommended part for new designs. They are almost identical hardware-wise but the bq78PL116 circuit example has a slightly changed slow charge control circuit using a FET instead of a bipolar NPN transistor as gate driver. I have not seen a description of the changes but I believe TI has had good reasons for the revised circuit.

Good luck!