OK, upgrades are not dependent on whether you booked thru a TA or directly thru Disney. The pixie dust falls where it will.
I'm not sure if you are asking about booking with DU specifically of booking with a TA in general as most of your questions are somewhat generic toward TAs although you phrase them as DU.
Your DU OBC is not going to evaporate today. Your quote may expire, but you can do it again tomorrow. I booked one vacation--B2B cruises thru DU. My biggest complaint is that the agent I was assigned to did not respond to e-mails promptly. I knew more about
DCL than they seemed to, and I got no service beyond the booking. I'm frankly not certain whether she lied to me or DCL lied to her at one point, but the info I was given was not accurate.
If you book thru any agent, you will make your payments thru that agent. You will be able to do your on line bookings, but you will not be able to talk directly to DCL for any questions--everything will be funneled thru your TA. Some TAs computer track all their reservations and automatically nail any lower prices or specials that you may qualify for. Some TAs provide an 800 number and will talk to you before booking to be sure you get what you want--cabin location, dining time, etc.; some deal only thru e-mail or snail mail or face to face. Some will call DCL on one line while you are on the other. Some will arrange private insurance for you (same prices as insuremytrip.com) and arrange flights if desired, others will book only DCL insurance and DCL air.
Booking with Disney, you can book on line or by calling them (there is a $25 credit for on line booking!). You can also get $50 OBC for using your Disney Visa card whether you book thru DCL or a TA. After you book, you can call them to be sure you get the deck that you want, request a specific cabin number, or whatever (but a TA can do all that for you). DCL isn't going to help you with anything you didn't book thru them...and they will only handle DCL insurance or DCL air. There's really no downside to booking directly with DCL. However, by booking with my TA, I get their excellent service plus an onboard credit.
OK, small example. I need to check in for my flight on line 24 hours in advance. Um....24 hours in advance, I'm going to be on the Magic, probably on an excursion somewhere. SO, I e-mailed my TA and asked if she could take care of this for me. She'll do the check in, I'll print the boarding pass when I get to the airport. She's probably not going to do it at 23 hours and 59 minutes, but it will be done and I won't have to worry about it.
If I had been on the cruise that spent an extra day at Castaway...causing everyone to need to re-do their transportation home...I would have called my TA (who has weekend and evening hours). One few minute phone call, and THEY would have handled the issues for me. No waiting for 15-30 minutes for the airlines, as people reported.