When wiring the shop the best way (in my opinion) is to run a large (#6) cable into the shop to a seperate smaller panel. Then run all your shop wiring off of that.
This has a lot of advamtages. This will save you a lot of wire going from the house panel to the shop. It makes adding shop circuits easier in the future. It puts a main shutoff in the shop and It puts all the breakers closer should you blow one while working. And don't think you need big amps in the shop either. A 60 amp panel is plenty to run a decent size shop with compressor, welder, etc.. Keep in mind you'l never have everything running at once. I have a 60amp panel in my shop - I've run my 220v welder, my 5 horse compressor and had the a/c running all at the same time and never blew a breaker. Of course all the big stuff is on its own circuit. And those three things have the biggest draw. A lot of people go crazy on house panels too. A 200amp panel is a waste of money. A 100amp panel is fine for pretty much any home, just buy a panel with a sufficient number of breaker slots. GFI protection ... personally I'd rather have GFI receptacles instead of breakers. This way you don't have to go to the panel to reset them.