Choptop, the battery issue........this is why a lot more dealersd are now installing a battery tender pigtail...hooked up to the battery, so that they can keep bikes charged up, and ready for a customer to pick it up. Our VERY GOOD local dealers...South Bound Honda (sponsoring vendor here) and South Sound Honda do this to every bike, which is a very good thing for customer service. If your dealer did not do this, and did not maintain the battery on your bike...shame on them.

To access that LEFT side cover to get to the battery, you do need to OPEN the left saddlebag. Just open it...then ignore it.
Then, you need to gently pull off the LEFT side cover...the one that has the chrome letters...F6B..on it. The gloss black paintyed section and the flat black section are screwed together, so they will come off as one unit.

If you have any doubts, there are 1001 pictures online of the side covers, and you can also go to the Honda OEM parts fiche, and look at a picture of it there.

Once the side cover is off, you will see the battery. There is a small black plastic cover that (thinks it is the gatekeeper) to the battery, and it is very easy to move out of the way, so you can have 100 % access to the battery. They "should" be no reason to remove the battery. Everything you need to do can be done with the battery still in the bike.

It would be very wise to go ahead and connect a battery tender pigtail to the battery posts...screwed on...in place, and then route the other end of that pigtail to a place where you can easily access it to connect a battery charger to.

Tip: before you reinstall that left side cover...use either silglyde or chapstick or anything like that...on all of the round and oval grommets, so that the posts on the backside of the side cover slide into the grommets easier.

Give that new battery a minimum of a 12 hour slow trickle charge, preferably less than 2 amps, and slowly bring it back up to full charge.

And...regarding the warranty issue, of them not knowing this bike has a 3 year unlimited mileage warranty...don't worry about it. With they way they are treating you so far, you will be finding a different dealer to take it to for warranty issues, or...you may never have a warranty issue at all.
All the other Honda dealers in the world will simply take the VIN off your bike, plug it into their computer, and they will know you are still under warranty.