Multiple Weapons, Extra Attacks, and Two-Weapon Fighting: If I have extra attacks from a high BAB, can I make attacks with different weapons and not incur a two-weapon fighting penalty?
Yes. Basically, you only incur TWF penalties if you are trying to get an extra attack per round.
Let's assume you're a 6th-level fighter (BAB +6/+1) holding a longsword in one hand and a light mace in the other. Your possible full attack combinations without using two-weapon fighting are:
(A) longsword at +6, longsword +1
(B ) mace +6, mace +1
(C) longsword +6, mace +1
(D) mace +6, longsword +1
All of these combinations result in you making exactly two attacks, one at +6 and one at +1. You're not getting any extra attacks, therefore you're not using the two-weapon fighting rule, and therefore you're not taking any two-weapon fighting penalties.
If you have Quick Draw, you could even start the round wielding only one weapon, make your main attack with it, draw the second weapon as a free action after your first attack, and use that second weapon to make your iterative attack (an "iterative attack" is an informal term meaning "extra attacks you get from having a high BAB"). As long as you're properly using the BAB values for your iterative attacks, and as long as you're not exceeding the number of attacks per round granted by your BAB, you are not considered to be using two-weapon fighting, and therefore do not take any of the penalties for two-weapon fighting.
The two-weapon fighting option in the Core Rulebook specifically refers to getting an extra attack for using a second weapon in your offhand. In the above four examples, there is no extra attack, therefore you're not using two-weapon fighting.
Using the longsword/mace example, if you use two-weapon fighting you actually have fewer options than if you aren't. Your options are (ignoring the primary/off hand penalties):
(A') primary longsword at +6, primary longsword at +1, off hand mace at +6
(B') primary mace at +6, primary mace at +1, off hand longsword at +6
In other words, once you decide you're using two-weapon fighting to get that extra attack on your turn (which you have to decide before you take any attacks on your turn), that decision locks you in to the format of "my primary weapon gets my main attack and my iterative attack, and my off hand weapon only gets the extra attack, and I apply two-weapon fighting penalties."
