High Command

"High Command" mode is accessed (by default) using Ctrl+Space. It will only be available if you have squads currently under your command, ie ones you have recruited using a Barracks.

To command a squad, simply enter the mode and then select a squad using F1, F2 as you would a unit, then middle-click on the map or in your main view to give them a destination. Ctrl+click can setup multiple waypoints.

Also try right-clicking your squad for options like stealth/combat mode.

To go back to controlling the individual units in your group, just hit ctrl+space again.