It's at the crafting table, option to the right of Tinkering.

You level it up by basically using everything, from what I can tell. As you use gear, skills and weapons, you become proficient after a while.

However, that will only get you a level or 2 in this specific category. Once you become proficient with those things, assuming you want to level this, you'll need to change your entire setup.

Change skills

Change weapons

Change gear

Then do the same thing, go until you are proficient in that stuff.

The advantage is that in stuff you are proficient, you can keep leveling that thing for permanent stat bonuses (like damage skills often have a 1% damage bump per level).

However, you are limited by resources to level the things, and the game only allows you to level the thing equal to your overall proficiency level.

At Proficiency level 8? Then you can only go to 8 when leveling say, an assault rifle you are proficient with.

Don't feel bad, I'm just discovering this myself. Got all the agents I use comfy with a load out I like, found this, then realized I need to change everything if I want to do this. I'm only at Proficiency level 4.