There is no linking your tickets like as Disney. Universal does not own the hotels. Most find a room only reservation and tickets bought separately is a better deal, price and change wise. Room only has a 5 day or less before check in, no charge to cancel or change. Packages from Universal have a longer time before charging for cancelling, and charge a change fee for any changes you make to the package. Plus, you can look fashionable sporting a lanyard, with your room card facing out on one side and your ticket facing out on the other. That way, all have their ticket and your room key acts as your express pass.
And yes, with a 2 night stay, say check in on Monday, Tuesday, Wednesday, when you check out. You will have all 3 days of express for IOA and the Studios. Yes, express pass for VB is separate.. I would by a 3 park ticket, for 3 days. You may not want to stay all day in VB, so you could go to a park if open. With express in the 2 parks, and early entry into one of the Potter areas, you can get a lot done in one park. Plus, with a three park, you can hop between IOA and the Studios by walking through City Walk, not a far walk, or take the Pottter train.
And yes, most of the time, RPR is the cheapest of the three onsite express hotels. But I would price PBR, and even HRH too. For my summer trip, my cheapest room is at the PBR. And, since room prices rise as time goes on, so I would book as soon as you are generally sure of your dates. Longer stays are generally discounted via a deal called Stay More, Save More. I have not seen a discount for 2 or 1 night. A room reservation will be secured with a one night charge. That is fully refundable until 5 days before your check in day. If within those five days, you owe thr total. Otherwise, you pay your total remaining, when you check out. While you can pre pay, you have to call in, and most do not do that. Also, if you call, the reservation people are good at helping with finding a good price, and will help you with any changes you need.
Take a look at the 3 resorts in their stickies in the Resorts board. They are a good wealth of information about each hotel.
I hope you have a great trip.