I wanna say HQ is kinda maybe straightforward, not sure if that's true or I just got used to it. At first it was unbelievably confusing. I still don't know where most the rooms are (doesn't help that we pick their location ourselves) but, luckily for us - knowing that is not needed! When you're needed somewhere, you get a marker that points you in that direction. Don't think there's ever a reason to go into Mansfield's office but you take the spiral ladder in the middle of big atrium and it's.. one of the rooms directly upstairs. One that's clean and has a bunch of fancy desks. With a hole in the wall until you patch it.
@jallard just take your time with it. It's not meant to be a chore. Exploring the place is up to you.
One thing you really need to know - workers need living quarters to be able to be sent to HQ. So you clean a bunch of rooms until something offers you to build them. Probably not enough scrap logistics to build the 4 person ones at first (that's why you recruit 1-2 fellas with really high endurance to send them to logistics dept and get more supply agreements - "scrap logistics" come directly from having more of them). Someone with 10 in a stat is ideal. I'd say put Preston to work.
Supply agreements are best with settlements that have a ton of extra crap. Like industrial resources, water, food, power.
Now, they have quarters (the top left corner in workshop mode shows how many workers you have and how many is your max until more need to be buil). Under every department on the top bar there's a number of max jobs for them. This shows how many you can send to a department. Those are made also from cleaning rooms then building logistics jobs (from workshop menu -> facilities). Stuff like storage closets, vending machines etc. You can upgrade those rooms from engineering after, to add more jobs or make it look cooler. Or add some new cool stuff.
Generally it's the same as other SS2 quests - just look at what the quest tab wants and do that. And if you really want to do nothing with micromanagement, use tgm like I suggested. I'd just be careful when doing 40 projects at once, most systems probably can't handle that. Wait for 3-5 (maybe 10) of them to complete, stand in game for a few seconds. Or minutes. The "How to HQ" and "Commonwealth Rising" quests get tedious if you really focus solely on them so again, just take your time. Look at what different departments have to offer, experiment a bit, and all that.