Ok so here are a few things I could really use some help clearing up.
Say a weapon does 3 damage(as in 3 dices) so you roll and see what comes up. No problem so far.
If someone has damage bonus… is that added as extra dices to roll or just plain added on top of the damage done?
When you soak armor point just flaty remove damage so 3 points of armor removes 3 damage while cover you roll dice??
Thank you 
If the bonus damage has a number with the Phoenix symbol its dice rolled. Bonus damage due to attributes is number of extra damage dice.
Armor just removed a set amount of damage. A shield on the other hand you roll to see how much damage can be removed.
Let’s say your character is using a broadsword and has 10 Brawn. The mighty sword does 5[cd] damage and the 10 Brawn is + 2[cd] for a total of 7 combat dice thrown each and every time the character hits.
Ranged damage and mental damage work the same way. If you do a Display (fear attack) that does 4[cd] and your Presence is 14, which adds 4 more, you’ll do 8[cd] fear damage.
Note that you’re also an Ancient Bloodline freak because you have a stat >12. 
Ah! I just had this question in my game only last week which made me validate we were doing it correctly…
Chapter 5 Page 120: Soak is divided into two categories, one for each type of damage: persistent and conditional. Persistent Soak is derived from things that are a constant for the character, such as armor worn or innate Courage, and it is always a static value. Conditional Soak comes from things that change frequently or are tied to the environment, such as the benefits of Cover or Morale, and it is always a number of §, providing a quantity of Soak equal to the total rolled on those §.
So my Breast plate is always 3 soak so 3 from any damage done to that area. But My Shield or the rock i am hiding behind is a conditional, and i have to roll to see how well it protected me.
That is correct. Armors are flat damage reduction, while cover and shields are having random soak value.