Very new to the game and I have lots of questions, but this one is at the top of the list:

If my investigator has, for example, both a machete and a .45 automatic in an asset slot and I make an attack, do I total up all of the attack and damage bonuses for that action?

Nope, both the .45 and the Machete have an "action arrow" (->) on them. You choose which one to use to take the action, you are only given the bonuses for that action (not for the action on the other card). Some cards will give you static boosts which will apply to every action you do, but if it has a -> trigger, then using it prevents combining it with other action triggers.

Yes. You would choose which weapon you want to use for each fight action. There are cards that you can use in tandem with an asset in play or an action you take to improve chances or increase the outcome. For example, if you have the skill card Vicious Blow in your hand you can apply it to your attack with whichever weapon you are using, or even if you decide to attack without a weapon. If you succeed, it will deal +1 damage.