In fire control you can select a different starting point in the geometry then just the beginning, even part way through a line.
When you select an area you can either choose start from loop which will be that entire Pierce and cut or you can start from line which will start part way through a loop.
In your case it sounds like you want to start from line down in the g code section after you select the area in the visualizer you want to start from.
Selecting from line will create a new Pierce and start point to the program.