Like normal Raspberry Pis running Raspbian. The config.txt file is the first thing the Raspberry Pi checks when it loads up off a PiNet based SD card.
The config.txt file can contain some key configuration/setup variables which can be used to set stuff like monitor resolution, overclocking etc.
A full list of the config.txt supported values can be found here.
Although a complex job to do in the background, PiNet allows for custom config.txt parameters to be appended to the default config.txt file then pushed out to all the Raspberry Pis.
xcompmgr libgl1-mesa-dri mesa-utils.