After you compelted the experiement setup wizard, AutoGate takes to you the gating side of the procedure.
As you can see, the samples are organized based on the grouping done in the setup wizard. You can change the naming of the samples or grouping by choosing Edit > Select Keywords. The grouping helps you when you choose to apply gates for samples within the group or across groups.
It is important to understand the tree, as this will go a long way in completing your analysis with ease. Navigate through the menus and they are mostly straight foward.
The functions can be accessed either via the File/Edit/.. menus at the top or using the right click menu.