For lodging check with the local tourist board office (Visit Scotland) for B&B's. My prefered way is to arrive in town and go to the office personally because in smaller towns they tend to know the inn keepers personally. In the larger cities that won't happen so you can call Visit Scotland and book. If you give them your budget they will find you someplace at that time of year.

Personally I stay at the Caledonian when I am in Edinburgh but I don't recomend it for a family on a budget (I'm not rich, just usually on business).

Best way to get around in the big towns is by bus. In Glasgow and Edinburgh you can get route maps and then you can buy day passes for the bus. In Edinburgh ther is a bus info shop for the Lothian busses on Hanover St. which is just off of Princes St. Taxis are fine but they can be expensive. If you are staying mostly in towns forget renting a car as it is more trouble than it is worth. If you are touring the countryside then get a car.

In Edinburgh take your son (and wife if she wants to go) and climb Arthur's Seat. It is a park that is only 10-15 minutes from Princes St. by bus (#31 or 33 if memory serves me right). The view is wonderful in all directions. When i was a boy my granfather and I used to climb it at least once a week. Unfortunately the sheep are no longer there, but it is still fun. I do it with my son when we are in Edinburgh.

Have fun and let me know if I can help. In case you didn't figure it out I grew up in Edinburgh and I am there frequently.