There are 2 directions you can take (in my opinion):
Ideal for newer more complicated HVAC systems
1. Retain your original climate controller and just tap the signals off the rotary dials and buttons and connect them to the Fusion Brain. This way you will retain all your factory climate features, and with a bit of logic you should be able to work out the temp from the position of the rotary dials so you can display it. Though you will just have to relocate you original climate unit and add a bit of interface hardware.
Good for older simpler HVAC systems
2. Remove the climate controller completely and add some temp sensors to the Fusion Brain. This way you can make up you own algorithm to control your temp, then you have complete control over the blower and temp. This method requires much more hardware interfacing.
Have a look at h3rk posts, he has done a huge amount of work on this subject and you should get some ideas from this guy.