That's a great time of year to go to WDW. Great prices, low crowds, great decor.
I've never gone through a
travel agency myself, and I think I get the best deals going. On the other hand, if you find a good travel agency, they will find the same discounts without you having to do much. Just like the one who sponsors this site.
I don't know of any place to really register to get discount codes per say, but this site has a news blip each day that lists codes, and Mousesavers ahs a newslatter that lists codes (they do have a special link for discounted tickets, but the discount is not huge.)
On the other hand, one of the best 'discounts' going now is to book the dining plan. If you are doing a honeymoon, I think it's the way to go. You do still have to pay for tips and alcohol, but the bulk of your meal is prepaid, and you can order anything you want off the menu (pretty much: almost any entree and dessert). There are very few exceptions. If you book the Dining plan, you pretty much have to get your tickets and stuff thorugh them, but it may be worthwhile. I haven't found an AP to be the best deal for my family in the last few years, but that may be differnet for another family.
Doing 'Disney math' can get fairly complicated: look at the price of your hotel, calculate meal costs, and park tickets for thenumber of days you want to go and the features you may want.
For a honeymoon, you may want to look at the 'wedding' info stuff. I think you'll find quite a bit of overlap between the kinds of things you wnat to do, and the kinds of things Disney offers for weddings. I'm not positive what kind of wedding info theDIS offers (IT might be great, I don't know) buyt I happen to know that the mousesavers page has added a wedding ideas section.
If you want romantic, consider a splurge at the Grand Floridian, complete with a meal at Victoria and Alberts, and maybe afireworks cruise. If that's not in your budget, then a meal at the Cali Grill is very nice. I think NO MATTER WHAT - CALL to book your trip, and TELL WDW that you are planning an anniversary and want help making it special. Anyone can dine at Cali Grill, but if you have a Disney coordinator help you, you'll get the best view and maybe some extra magic.
Any of the Deluxe resrts would be great for the kind of trip you describe, but if that's not in your budget, I'd pick POFQ, CSR, maybe CBR, or maybe the Magnolia Bend side of POR (Though POR is personally my least favorite moderate resort, it does have a romantic aspect). I'd steer clear of the values myself, but if I had to pick among them I'd pick ASMu.