esentially if you are getting the bottom end rebuilt they will depending on what you need:
first they strip all the parts off the block
bore (if you are going with bigger pistons)
deck (make sure everything is nice and level)
hot tank
as well, they should rebalance the crank and clean up and reinstall all the parts that ask them to install (bearings, rods, rod bolts, pistons, piston rings, etc)
the above is for the bottom end
if you get the entire longblock rebuilt (head+bottom end)
they should port out the head if you ask them to (increases air flow, resulting in better spool times, etc)
they should also reinstall the remaining parts (valves, valve springs, cams, etc)
so to answer the above question, when they do a proper rebuilt, they should take everything apart and reinstall everything to make sure everything is working properly