Upgrading your gear is going to be essential for your progression and trust me it is no easy feat to do when you have to take into consideration of all the other things you will be doing in the background. That being said it is something that you are going to want to prioritize as you hit each new set so that you can continue you on with the other advances that rely on you hitting certain milestones.
Upon hitting certain milestones in your gear upgrading you will be rewarded with these set bonuses. Typically they are the same for each set but you will notice a lot of improvement if you are willing to invest your garnets into these upgrades.
Realistically you will want to max all of your upgrades over time but it is very important to at least get each of your gear sets to +11. Typically after this stage it starts to get expensive as far as resource cost goes.
Though it is expensive to max, these bonuses are worth it in the long run.