In the vicinity of your HQ, Open the commander menu and scroll through the pages until you find an option that says "set rebel loadout". You click on that and it'll give you a list of each infantry role (Rifleman, auto rifleman, light AT, etc.) . You just click on any of them and it'll open the arsenal. That's where you'll select exactly what weapon and armor you want them to have. Just remember that you'll also have to equip them with whatever magazines, grenades, medkits, etc. that you want them to carry, while you're in that screen.