He can still have lots of fun and do lots of things in a wheelchair, so don't worry. If you are leaving in 2 weeks, you won't be there at at really busy time. That helps a lot and you may find that your wait for many rides/attractions is very short.
First of all, transportation: You won't have any trouble staying at BWV. You can walk to MGM and Epcot from there or take the boats. The boats may actually take longer than walking. It's about a 10-15 minute walk to either place. The boat ride is at least that long once you get on the boat. Most buses are equipped with wheelchair lifts and tiedowns. Just have him park about where the rear door of a stopping bus will end up and when a bus arrives, signal the driver that you want to get on. The driver will open the back door for your party and direct you what to do.
For rides in the park, almost all the lines at AK and MGM are wheelchair accessible (This is called Mainstream Access), so he will wait generally wait in the same lines with everyone else. You can also use fastpass, which will help shorten your wait in line. The CM at the ride entrance can help direct you to the right place and give you information about boarding.
At Epcot and MK, not all rides have total wheelchair accessibility in the regular line. For those rides, there is an alternate entrance for people traveling with wheelchairs. Often you will wait in the regular line until just before the line goes to the boarding area. At that point, your party (the person in the wheelchair plus us to 5 members of their party) will be directed to the alternate entrance. There are a few rides where you are directed right to the alternate entrance (an example of that type of ride would be Small World).
Here's a link to the DIS page about touring with a mobility disability. It includes a list of rides with Mainstream Access (scroll to the bottom) and lists of rides/attractions where the person in a wheelchair needs to transfer into a ride car and ones where you can stay in a wheelchair for the whole attraction.
If he can walk a few steps, he will be able to transfer to any ride. The CMs at the ride can help with doing things like moving the wheelchair after your party gets on, steadying the wheelchair or slowing /stopping moving walkways temporarily while your dad gets on. They can't actually lift or physically transfer anyone though. Be ready to tell the CM what sort of assistance you will need (they may have pixie dust, but they don't have ESP)
The "special needs" (wheelchair) boarding area is often at the exit of rides. This gives a little extra time and space for boarding and the CM has more control of the ride from that station. For rides where you have to get into a ride car, this also puts the wheelchair at the exit point.
Ask as many more questions as you need to get everything clear. Here's some pixie dust for a great trip.
