We did WDW with my MIL, FIL, SIL, and BIL last summer, and it was a first trip for all 4. I was VERY nervous - they are from the West with no humidity and are not big walkers. It definitely took a lot of effort and planning on my part to make sure we had all our ducks in a row, and A LOT of convincing why taking a midday break was necessary and having a resort day was a good thing, but in the end it was a great trip.
We did a split-stay at POR/YC, but had 2 rooms, which (as you point out) was great. The first two days, they were very "we need to do everythign as a group" which DH and I kept trying to get away from: we felt more like doing first part of the day together, break up after lunch (for those that want to go back to the resort), meet up around dinner or even later in the evening. On our resort day, we all hit SAB and we finally broke into our respective couples for the better part of the afternoon, and met up for our Fireworks Cruise that night... it worked so well! Everyone did different stuff that afternoon, we weren't stressed from each other, and it was just relaxing - not to mention a wonderful cruise. The last two park days, we did the AM together, and broke up around lunchtime. One day, we met for dinner and split up again, the next day we met at the resort after dinner and went over to MK for EMH together and stayed together until 2 am.
I HIGHLY recommend spending some time away once your parents 'get' the way things move at Disney - we spent the first day explainng Fast passes and Dining Plan so they would be able to use both. They will tour at a different pace and may want to take in shows that you and family don't, or they may want a midday break when you are ready to press on. Just make sure to schedule some full family meals or times so that they don't feel 'slighted' but explain the virtues of some QT where they can feel like kids again with the magic!