You set up peg groups in the first tab.
A peg group is an independent set of pegs that are worked with on their own.
Peg groups can be used to use to store separate groups of pegs for check surveys or other kinds of operations where you do not want to clutter a particular group with another set of pegs.
You can toggle between peg groups by clicking on the current peg group name at the bottom right of the main application dialog for MineModeller:
