Focus on battle
Leave cons be and don't waste time with them, if you are engaged, fighting is your main priority.
Repeat is good
This alleviates some stress from having to constantly babysit the factory, but watch out if someone has found a counter. If that happens change the composition immediately.
No two factories are the same
What can counter one thing may not necessarily counter another, and this is true for factories. Avoid using the same counter composition repeatedly.
Close? Or Far? Where should I place my other factory?
If your factory is either a Gunship or Air, it is better to place it far away in the back as the distance is often negligible. The biggest one is for slow ground units, should it be close to the front line, or far? If you are close, an attack can come very quickly towards the factory and destroy it. However, reinforcements arrive much quicker and may be able to destroy an incoming attack. If your far, it is opposite, as the factory can not be attacked easily, but the reinforcements will take some time.
If you switch the factory, you can surprise the enemy and destroy their units quickly and efficiently. However, making the second factory does slow down production and new units will take some time to be built. However, if this can win the game, use it. Once you do this, leave the old factory so in the even the new one is destroyed, the old one can build again. This is perfect if you swapped to air as the enemy will probabaly have anti-aircrafr, and will lose lots of units if you attack with normal ground units.
Learn the factory
If you have a favorite factory, learn everything about it and how it is used, how it can be used, and what it is best at. These do help in combat.