this is all going to be personal choice, so what suits me, may not suit you, or anyone else with an annual pass.
With annual passes we look at the price of room only at the DLP onsite hotels (in certain seasons, as I said before, Disney/Expedia/ebookers etc has some great deals for onsite rooms). I'd also call DLP and ask them for their room only rate with annual passes (but its been about 5 years since I've personally found them competitive doing room only at their own hotels).
Then I'll look at the associated hotels, booked through their own websites or other agents (again, expedia, travelrepublic, alpharooms, ebookers, hotels.com etc etc etc).
To be perfectly honest, apart from first-nighters in val d'europe or bussy st george, I've not gone further offsite than the associated hotels for the bulk of my trips. Not to say I never would, but I've always managed to find either an onsite room, or associated room, in my budget.
Then of course, you could always (again, at certain times of the year this will be a better deal than at others) book one adult in on a discounted tickets/hotel package through Disney, then add the other adult to the room at check-in at no extra cost.
That, in a nutshell, is how I go about booking accommodation for DLP

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