I always start planning early. My family swears for me that the planning portion is half of the fun. Here is my suggestions:
1. When flying I decide what price I am willing to pay. I check regularly at the various different airlines and when I find the price I am willing to pay I book. I get a price I am happy with and the times I want. I know sometimes there are great last minute deals but wouldn't want to risk not getting a flight or paying something very high.
2. I personally don't like switching hotels even on Disney property. For me it is just too much work to pack up everything and move. When I travel there is me, DH, two DD, DS and my mom whom is handicapped. I like to stay put once I am at Disney. I guess if you are going to visit Universal though it might be worth the hassels of moving for front of the line access. I would either do this at the beginning or end so that there is only one move involved. Also if you are visiting both places you will probably need to rent a car instead of using a shuttle or limo service. Neither Disney nor Universal provides transportation to the others parks.
3. I always have my next hotel in mind when I return from Disney. I don't make any hotel reservations through WDW until codes come out. I think everyone booking ahead of time makes it more likely that there will be no codes. I do usually book at the Dolphin or Swan at the teachers rate as my back up plan. That reservation is not then part of WDW reservation system. Also if there are no codes I get to stay deluxe for less than the cost of a moderate at Disney.
Relax and enjoy yourself. Those of us who love Disney often find planning the trip to be alot of fun.