So I just bought the equipment pack and was looking through the cards, what is the difference between the bonus and bonus token cards and how do I use them?

I suppose you are talking about "Bonus tokens" and "Bonus (equipment) packs". The "Bonus packs" are complete equipment packs with 3 tokens belonging to a specfic character and were usually released later than the character and his "normal" equipment packs. During game setup, you may choose a "Bonus pack" instead of the character's Combat pack, Stamina pack or Command pack.

"Bonus tokens" on the other hand are single tokens that do not belong to a specific equipment pack or even to a specific character. Some of them may be used by any character or any character belonging to a certain faction. During game setup after choosing equipment packs, you may exchange an equipment token of your character's equipment pack with a "Bonus token". Just keep in mind that each character may only use one "Bonus token" and your team may not use more than three "Bonus tokens". Furthermore, you may not use the same "Bonus token" as your opponent. If both of you want to use the same token, roll a die to decide who gets to use it.