I'm making a character who will be using an Ares Alpha, but I haven't been able to find a ruling on what skill is used to shoot an underbarrel weapon. Since the Alpha has a UGL, does that mean that I need to take Heavy Weapons to fire the UGL AND take Automatics to shoot the rifle itself?

AFAIK, yes you need both skills. If you think about it, the grenade launcher still works exactly the same as it would if it were just a grenade launcher. Like, if you didn't load any rifle ammo, you'd just be using a grenade launcher, so obviously it should use the same skill that any other grenade launcher would.

Underbelly Grenade Launcher would use Heavy Weapons just like any other Grenade Launcher. *Ploop* *Whistle* *BOOM*

In addition, a MasterKey system (Underbelly Shotgun) would use the Longarms skill.