--I have my watch set to mirror most things, like Airplane Mode. But it's not.
When mirrored, the Watch will go into Airplane mode when the phone does. But since the Watch is in Airplane mode, there's no way for it do know you've taken the phone out of it. (I hope I understood your situation correctly.)
--What is the benefit of having "background app refresh" going for watch apps? I don't allow it for any apps besides Fantastical on my phone, so is there any reason to do so on the watch?
Most Watch apps are now supposed to reside on the Watch instead of phoning home to the phone for functionality. Background refresh as you know, allows the app to 'open' already updated with the latest data. So you'd want to enable it for any apps that you did so on your phone, that have a Watch component.
--My watch software is 3.1 and it says it's at the most updated. How do I update that? Do I have to connect it to the charger to get any of the changes to apply? Or is it automatic when I do something in the app?
You have to update the wOS manually in the Watch app, select General and Software Update. It will tell you that you have to have Internet connection, your Watch has to have a 50% charge, and it has to be on it's charger.
--Also, when I "make" a new face, it doesn't seem to change on the watch very quickly even when I set the new face. Does the watch need to be on the charger for that? And how do I put new faces on it? Like is there a place to d/l new faces other people made on it? I don't see much of anything in the app store for watch... And how do I do that?
Ok. The Watch doesn't have to be on a charger, and it takes Apple to make a new face. Or template for a new face. You can't download any from anywhere. (That could change if somebody jailbreaks wOS.)
You can make a new face on the Watch or in the Watch app on the phone. It will take a
short time for a new face to show up on your Watch when made in the app. The Watch doesn't need to be on the charger, but the face does have to move to the phone. Making it on the Watch is instant.
On the Watch: from your current Watch face, do a force touch and you'll see the name of the face and Customize. Swipe left alllllll the way to the right end of the face parade and you'll see the big plus sign and New. Force touch that and you'll get the first template for a face- Activity. Use the crown to scroll through the various templates until you see one you want to add. At this point, it's pretty intuitive to change colors, face designs, and complications. Force touch each complication you want to change. Use the crown to scroll through the options. You can turn an unwanted complication off if you like. When done, tap the face or the crown and Bob's your uncle.
In the app, it's a little more complicated, but apparently you've got that down.
About the screen protectors— I'm pretty careful by second nature with my Watches and watches, but I do want to use protection. It's the responsible thing to do. The curling edges seem to be the real problem with these. It should take more than overnight to 'bake'. Does your version use water to activate (old school, i guess) or is it just dry adhesive? Maybe you need to do the Mr. Miyagi thing with your hands, then palm for an extended period. Or put some folds of cloth over it and wrap in with some string or ribbon, given the holidays, and let it bake that way.
I hope these work as I'd like to cover the screens.