Some things to remember when Commando healing:
1. Pop off SC with fair frequency, especially after you get Kolto Bomb. The damage shield it gives can help loads if everyone is taking a lot of damage. Don't ever forget it's there, its very important to use. It also gives back 2 ammo, makes you do 10% more healing, and lets you get off about 4 AMPs in a row before it runs out if you need to pump out some burst heals.
2. Once you get Kolto Bomb, you should use whenever it's off CD after you get the talented healing buff it gives unless you are starved for ammo. The healing buff it gives and the shield buff with SC are too good to pass up, you want to keep them up as much as possible.
3. The main time you will find yourself running out of ammo early on is when using MP over and over again. Keep in mind this heal uses quite a bit of ammo (3 charges each) and if you spam it you will find yourself using Recharge Cells every time it's off CD. This becomes easier after you talent AMP to take off 2 ammo cost for MP every time you use it.
4. Always, always use CSC while healing. I'd recommend spamming Hammer Shot on the tank all the time, even when he has full HP, as it lets you pop of your SC buff at a moments notice for the next pull. If you are doing 100% healing (no DPS on the side) and aren't using CSC, you're doing it wrong.