Okay, what'd I do?

[HundertzehnGustav]

Let me read and take care to understand all you say...

I can now and extract/enable the mods I want
open Commander and start a new career,
load the game and select that career,
Go out on one patrol, complete it, return to base, and exit the game,

the "complete patrol, return to base and exit", THAT is what you do.
You want to enable mods? Do it before you start a career or when you are at home. And ONLY there.

-Tip. your crew has few qualifications when they start their war. Make of your first patrol a very short one, dont even leave the harbor area. Then you can "manage your crew" in commander and give more qualifications.

The other thing that confuses is me
Once I return to base, the game auto-saves the career, so if I've finished the patrol and returned to base, I don't need to do anything but exit, right?

no...?

The game does not autosave anything.
You do the saving.
Either somewhere in the ocean, in the middle of the action
Or Once you return to base, (within a couple of miles of the harbor) you hit the escape button.
The question is then asked:

• you wanna exit simply
  (lose all progress since the last save point/the last time you were at your desk)
• or you wanna dock at your harbor XYZ (save your progress, and then walk off the Uboat and into your office, report to your boss and get the renown for your work )

BUT - if I do a save when I'm NOT in base, then I shouldn't make any changes to mods until I go back in, start from that save point, and play until I finish up that patrol and am back in base again.

correct. You not at home, dont touch any damn files!

*hands The Lady a cold Beer*