1. You only take a penalty to attack if you are actually two-weapon fighting. If you decide that you only want to do shield bashes that round and not attack with your actual "weapon", there's no penalty.
2. Shield Master only removes the penalty to attack from the shield, the main weapon will still take the appropriate penalty from two-weapon fighting.
That hadn't occurred to me, thanks for pointing that out. I'll have to keep that in mind, in case I come across a situation where I may need to know that!
You'd do this in situations where you couldn't take a full attack action, so in any place that you have to move and take a Standard Action (single attack).
That's what I figured, but I just wanted to make sure. Is there any way to remove the penalty from the main weapon, if I do both a main attack and a shield bash? Or am I stuck with that penalty forever?
The only way that I can think of would be to be the Two-Weapon Warrior archetype of the fighter. You would have to wield two light weapons, so a Light Shield and a Light weapon (such as a light steel shield and a short sword). The penalties are reduced at l11 and l15.
Other than that, you'd have to 'negate' the penalties through weapon training, feats, and enchants (and maybe buffs from your party).
Is there any way to remove the penalty from the main weapon, if I do both a main attack and a shield bash?
Option 1: Use a light shield instead of a heavy shield. This counts as a light weapon, so if you use a light shield in your off-hand, and have the TWF feat, the penalty is only -2 to your other weapon.
Option 2: Use the shield as your main hand, and the other weapon as your off-hand. If the other weapon is light, it's only a -2 penalty.
Option 3: Cheese to the max by using two shields. The shield bonus to AC will not stack, but you can bash with both of them without taking penalties. You may get dirty looks by doing this.