Congrats! DH and I did our "Disneymoon" last October. You'll have a blast!
Anyway, the two parks we usually visit more than once is MK and Epcot. MK because it has the most rides, and Epcot because it's so freakin' huge, plus the restaurants and Illuminations (our fav nightime show!). Hoping to Epcot from MK is easy, just take the monorail (you'll have to switch trains at the TTC, though). The other parks to Epcot can be a bit tricker because of the busses (but I think you may be able to take a boat between MGM and Epcot, but I'm not 100% on that, I've never done it).
We find that if we get to AK at open (usually 8 AM) we are done by 1 or 2. We usually keep AK for our last day, leave the park mid-afternoon, head back to the resort, pick up our bags from the bell hop (we've checked out already) and then just go to the airport. At the park, I recomend the safari (must do) the Jungle Treke (more animals), the Lion King show (see this if you do nothing else!) the Dinosaur ride, Kali River Rapids (water ride, you'll get soaked, skip if you don't want to be wet), Tough to be a Bug 3D movie, and of course the new Everest thrill ride.
At MGM, we can stretch it in to an all day event by going on ALL the rides and seeing several shows, then taking a loooong time at dinner (we love the Brown Derby) and then going to Fantasmic. But, I think for our next trip we'll sleep in and not go to MGM until noon. We've done all the smaller attractions so many times that we don't feel the need to repeat many. We do want to stay and see Fantasmic at night, though, and I strongly suggest that you do, too. RnR and ToT are the best thrill rides in all of WDW. Other than that, I recomend the Beauty and the Beast show, the Little Mermaid show, Muppets 3D, Star Tours, the animation tours, and the new car stunt show. I'd do the backlot tour and the Great Movie Ride again if I had time, but wouldn't be upset if I didn't get too (they are good, I just don't feel the need to do them every trip!).
For a six day visit (I assume this means 5 nights, correct me if I'm wrong) this is how I'd plan it, if it were me.
Day 1: take 1st flight of the day to Orlando, arrive at hotel, check in, then MK rest of day
Day 2: Epcot
Day 3: Resort day, relax at hotel. Then DTD in the evening
Day 4: MGM
Day 5: MK, then hop to Epcot
Day 6: AK until 2 or 3, then head to the airport for late flight home
If you want to go to a water park, you can do that in place of the "resort day" on day 3. If don't have a late flight on your last day, then you can do AK first thing one morning until about 1 or 2, then hop to MGM for the rest of the day, staying for Fantasmic. It would look like this:
Day 1: take 1st flight of the day to Orlando, arrive at hotel, check in, then MK rest of day
Day 2: Epcot
Day 3: Resort day, relax at hotel. Then DTD in the evening
Day 4: AK, then hop to MGM
Day 5: MK, then hop to Epcot
Day 6: Depart for home
Also, you may not have an early flight on the day you arrive. If you are going to get to the resort after 3 PM or the park isn't open past 8 or 9 that night, you may not get enough time in at MK to make using a day of your pass worth while. In that case, I'd do this:
Day 1: Spend evening at DTD
Day 2: MK
Day 3 Epcot
Day 4: MGM
Day 5: MK, then hop to Epcot
Day 6: AK until you have to leave for airport
If you arrive late on day 1 and have to leave early on day 6, then I'd do this:
Day 1: Spend evening at DTD
Day 2: MK
Day 3 Epcot
Day 4: AK, then hop to MGM
Day 5: MK, then hop to Epcot
Day 6: Depart for home
In all cases, whenever I go to WDW (or
Disneyland, like we are next week!

) I use a spread sheet to help me plan. In the first column going down, I put the dates. In the first column going across, I put "Morning" "Afternoon" and "Evening" going across, this makes a grid.
Then on each date going across, I put what park (or whatever) we will be at in each "Morning" "Afternoon" and "Evening" column. If I'm going to make a restaurant reservation, I'll note what restaurant and what time I'll be requesting in the appropriate box. This gives me a visual plan I can look at and play around with until I'm happy with the balance of what parks we will be visiting when, and helps me plan my restaurant reservations and any other activities. I also use it to budget meals (it's a spread sheet afterall, may as well use it to add some stuff up!).
Now once you get there, you don't HAVE to follow the plan. But we find it works great, it keeps us from looking at each other and saying "what do you want to do?" "I don't know, what do
you want to do?". I've never felt spontinaity works well at WDW, unless you've been two dozen times and you don't care if you see everything in this particular trip.