If you book an extra night then yes you will have to checkout/checkin at the front desk sometime during your changeover day, but if you make sure that your two reservations are listed as linked/continuing, then it's most unlikely they will ask you to change rooms, you'll just need to have your keycards updated. The only possible problem is if you are on a dining plan, etc. as that won't carry over in the second reservation.
38 sounds like a good choice, it's really not that long a walk to the main buildings (5 minutes tops, probably less). You can get buses from the South Depot or the outer ones, but personally I've always taken EMH buses from South. You should be OK at the other stops though if you want to try that.
As long as your reservations are linked, and you have asked for nearby rooms, they should normally put you all into the same building. You can always fax them before you arrive to confirm too.
Andre