The Clone Commander is a powerful and useful unit in the hands of someone who knows how to use them properly. The following series of instructions is geared towards players who will routinely be able to unlock the Clone Commander by getting enough points- in short, you are no novice to the game.
You'll find that the Clone Commander is armed with a chaingun as primary weapon and a blaster pistol as his sidearm; for secondary techniques he is equipped with Rally (providing a defense bonus to nearby troops) and a Recon Droid. Since you cannot spawn the Clone Commander without engaging in battle slightly beforehand, you should have a decent idea of where the battle is headed by now.
Resist the urge to charge mindlessly into the fray, firing your chaingun at will. You will die the majority of the time while attempting this strategy. Instead, depending on the various levels of urgency with which you are using the Clone Commander, you can do one of several things.
If you're winning by a large margin, then feel free to disregard the above advice. The chaingun is one of the most powerful weapons in the game once warmed up (which takes a moment), so with large margins of a lead you should take the advantage and enjoy being one of the top units. Your team also will not be needing you, so using Rally is unnecessary. You'll avoid using the blaster pistol as well, because the chaingun does not run out of ammunition.
If you're in the lead but victory is still "up for grabs", so to speak, you'll want to use the Clone Commander to create a larger margin for your team. Since dying repeatedly defeats the purpose, you'll want to take greater care when moving around the battlefield. Unlike the first scenario, you will need to not charge mindlessly, but be a bit smarter about how to engage. The chaingun will be your primary method of attack when you first move in, so if possible try to limit the space and areas of cover of the environment. The ideal size is the hallway running along the Jedi Council Chamber on Coruscant: Jedi Temple, or even the Jedi library on the same level. What you want to do is maximize the chaingun's accuracy without giving devastating units such as the Engineer a chance to get close.
What you will need to do before moving out, however, is to utilize the recon droid to scout ahead. This droid is almost completely worthless for attack (as it is frequently targeted by the enemy, with excellent accuracy most of the time), and when it is set to detonate it can still be easily destroyed. The only substantial advantage it offers is to give you an estimation of the size and composition of the enemy force you are about to engage. Be smart when using the recon droid. It makes no sense to determine that there are three Destroyer Droids around the corner, and to subsequently charge anyways. The whole point in determining what awaits you is to give yourself optimum chances for a successful attack.
When you are facing the enemy and are losing by a small amount, all is not lost. The Clone Commander can easily turn the tide, if used appropriately. To snatch a victory from the jaws of defeat, you will need to display expert use of the Commander. You'll want to recognize that the chaingun, while wonderful, is by no means the be-all, end-all. In fact, if you are able to get the Precision Pistol, using it in conjunction with the chaingun will see the best results. The chaingun is an excellent means of dispatching multiple enemies quickly, but the pistol has a much higher probability of headshots and will deal more damage per shot. Additionally, if units are advancing one at a time, the chaingun does not warm up well in succession, meaning that you will soon be overwhelmed. The pistol is much more effective at dispatching lone units.
Some final notes in this scenario are that the Clone Commander, while powerful alone, still works best with other units. Communicate with your squad, and draw as many units together as possible. Scout ahead with the recon droid, and when you come upon a sizable opposing force, use your Rally to up your men's defense. While it doesn't see a particularly higher rate of success, be aware that every bit helps. And those that your men cannot clean up on their own, you should wipe up with ease. Be sure to include Clone Troopers and Heavy Troopers in your makeshift squad, as they will launch Thermal Detonators (which are lacking in the Clone Commander's arsenal) at any droideka that happen to show up.
When you're going to lose with nearly absolute certainty, you can choose one of two fates. Either you will try to wreak as much havoc as possible on the enemy before the end, in which case no strategy is necessary, or you will try for survival in the face of the opposing tide. If the latter is the case, you should refer to all of the above strategies. You'll find that optimum use of all of your tools will lead to the highest rate of survival, where applicable (obviously the Rally bonus is only useful with troops nearby, etc.). If you are trying to just wreak havoc and take as many down as you can before dying, you should position yourself in as small a space as possible, preferably with a clear view of all means of entry without having to turn. Also, if an Ammo Droid is nearby, you can attempt to pick off enemy units with the pathetic blaster they support, immediately replenishing your supply of droids as they are launched. And, in this event, a mindless charge can feel somewhat rewarding.
The Clone Commander, while an excellent unit, is by no means invincible. Be aware of his weaknesses, and do everything in your power to maximize the strengths of the unit. Above all, use your head. The Clone Commander, despite his powerful approach, has a great deal of finesse which must be mastered in order to effectively use him. Be confident with the chaingun, but be aware of its recharge rates and strengths over distances. Know the pistol at your disposal. Use the recon droid with intelligence, and the Rally when applicable. Your skill as a fighter is not enough; you need to develop intuition and strategy to be a proficient Clone Commander.