Armies

Where are you getting stuck? Take your units together (without the commander) and move them just close enough to shoot the enemy, sometimes taking single steps closer so that more of your units are shooting. An even better approach would be arrange your units a certain way so that when ordering them to go to a spot, they all arrive at the same time. When need to take out shield generators, place your units around it, then tell the commander to go destroy it, as soon as he is done, move him away (keep him selected for this and have good timing).

My strategy was to send all but the commander in a big clump into the middle of groups of enemies, and that way they were all gone way before the end of the mission.

First, your soldiers don't shoot while moving. And when you tell them to move into the middle of a group of enemies, there will be a lot of enemy fire before your troops return fire.

In level 2 (in Easy mode), destroying the second shield generator always kills the commander, no matter how many units I try to pack around it.

Keep your commander selected and as soon as he is finished, move him away. The enemy do always target the commander first, I think I might change it to a bit randomly.

The hint worked very well but when I unlocked the third generator the guys shot the commander before he got away even though I was clicking him away. Maybe you can slow down their reaction time or something. How did you beat that level?