I am currently building a dagger tossing Investigator. I am curious with multiple daggers what are the correct calculations for thrown weapons.
What do I use for my Attack Bonus and do I gain a minus to anything for throwing a dagger?
Simple formula: BAB + DEX modifier. That is your to-hit bonus.
You may have other situational bonuses, like the Point-Blank Shot feat which adds +1 to hit and damage within 30', or Weapon Focus(dagger) which would give you +1 but only with daggers. Or others as well. When those situations apply, you add them as applicable.
Don't forget to add your STR modifier to the damage but not to the attack roll.
You'll also have to remember a few basic rules:
Range Increment: For a dagger, it's 10 feet. This means you take no penalty throwing it up to 10', then add -2 for each additional 10' after that, up to a maximum of 5 range increments (50 feet) which is your maximum range throwing a dagger. So throwing a dagger at someone 35 feet away would apply a -6 penalty to the attack roll. The Far Shot feat can help reduce these penalties.
Throwing into Melee: If your target is fighting any ally (even NPCs you don't want to hurt), you automatically take a -4 penalty on ranged attacks. You can eliminate this penalty with the Precise Shot feat.
Cover: If there is stuff between you and your target, including your allies, you add +4 to the target's AC. There are a lot of rules for deciding if your opponent has cover. Your GM will do this for you but you should be careful to make sure you have a good line of attack to the enemy.
The only other things I can think of here are the action to throw (which doesn't get weird until you're tossing around spears or tridents) and how quickly you're drawing them. If you're hoping to use iterative attacks down the line, you'll need Quick Draw, if memory serves.
And if you want to fling both daggers at once, say hello to Two-Weapon Fighting's penalties.
Make sure to look at items like the Blinkback Belt and the Whetstone, they can help.
Traits like River Rat can give a small damage boost. Don't be put off by the crappy range, 5 foot adjust and throw is pretty sweet, you basically get to USE Point Blank (one feat for a +1 to hit AND damage? Yes please!).
Quick Draw will be very useful later, but I would take Point Blank first.
Happy stabbing!