After you've checked in, where you'll also receive your boarding pass, unless you did that online before you left home, you just go on through security and to your departure gate. At that point, since you went to the main check in desk, you should have no problems, unless, of course, one of your bags is too large for an overhead bin, or to go under the seat, but it seems they'd catch that at the main desk, before you ever got to the departure gate.
I’m confused now...so you can get the gate check tag at the normal check-in point? And then just hand it to them at the gate?
I’d be checking one bag the normal way...my suitcase. But I’d want to gate check the guitar.