Installing a "battery controller" on my desktop motherboard
You've asked two questions.  Paraphrasing:


  I plan to do a 4S2P lithium-based battery system design.  Is my plan
  OK?


It's certainly possible, but it doesn't sound like you've put any effort into designing a battery management system, which would need to address charge control, discharge limit, current limiting, temperature monitoring &amp; management, etc.  If you haven't worked with Lithium chemistry batteries before, consider using a cheap, commonly available lead acid battery in your initial prototype - they're much easier to work with, are more forgiving and are generally safer without explicit battery management.


  I want to be able to monitor battery SOC (and do other thing) via
  Windows OS.


Easy - simply design the microcontroller-based solution you mentioned in your post, then connect the microcontroller to the motherboard via RS232.  You'll need to design a simple communication protocol over the serial interface and will need to write a windows application to display SOC and provide whatever features you want, but the process is very straightforward.