Yes, if the green square is filled it means it's on. Most companions do not have the ability turned on if it is an ability that they do not start with. Take Corso for example: he only has one or two abilities when you get him, and when he gains others as you level you have to turn them on. But when you get Guss he will have all of his abilities and they will all be turned on.
You only have three real "ranged" abilities as Scoundrel - your basic attack, Vital Shot, and Thermal Grenade. Any other 30m skills you shouldn't use. Everything else is 4-10 meters, which makes it a melee class. The only attacks you really need as a Sawbones Scoundrel are Backblast, Blaster Whip, Blaster Volley and Vital Shot. Only one of those is a 30m, two are 4m, and one is 10m.
Since you have Bowdaar you're obviously past Nar Shaddaa, which mean you should be mid-20s at least. At that level range your companions should have the majority of their abilities. Each tank companion gets one 3 target AoE, and one multi-target AoE. The 3 target one comes pretty early, and it should be the 4th or 5th abilities on their tray. Usually the second to last ability they get is an AoE taunt, which makes leveling a breeze when they use it. Once your tank gets the multi-target AoE (EMP Blast for Corso and Wookie Roar for Bowdaar) though you should really have no problems whatsoever. I forget what level they get this at, but if you don't have it yet you should have it very soon.
Also, make sure they're in the tank stance. If you HoT them you will pull aggro at first, but once your comp hits them with an AoE they should pull aggro. Putting the HoT on yourself too can help with any aggro you do take. On my Operative I just HoT'd me and my tank, stealthed up, Hidden Strike > Shiv > Carbine Burst spam. And things die in seconds.