New Project with Mesa 7I96 and THCAD-05

ok I just tried it and now it works i can get into the gui. Now the next question do I need to run the 7i96 configuration tool to set it up I already set it up through pncconfig? How will the THCAD-5 connect to and if I wanted to add the THCAD-10 later how will i activate the other encoder input?

No, the 7i96 configuration utility and pncconf are two different configuration tools.
Any changes now should be done by editing the hal/ini files or running the calibration
utility

If you have a single THCAD it connects to the 7I96 encoder inputs

To have multiple THCADs you would need to install the 7i96dpl.bit firmware
and then the next THCAD connects to the encoder "B" pins

On Mesa's website for the 7i96, there is a zip file to download. In it there will be a bit file that the file name included 7i96 and ends in pl.bit
So you use mesaflash to download it to the 7i96.

I saw the Mesaflash how do I get that installed.

To get the latest version you would need to fetch the source:

github.com/LinuxCNC/mesaflash

and build/install it

There are instructions for this on the bottom of the github page