There are a number of methods that give a good result... Probably the easiest is using light springs in place of the standard valve springs...
change out the valve springs, set up the valve train, use a solid lifter & set it to zero lash, set up a degree wheel, (zero TDC) so you can keep a close eye on how much you turn the crank.. Set up a dial indicator so it's straight in line with valve travel then bring the engine up to 10 degrees BTDC & check the valve travel then go to 7 degrees & recheck, again at 4, 2, 0, 2, 4, 7.... Do this for both valves...
A safe rule of thumb is .080-inch for intake valves and .100-inch for exhaust... Plenty of guys run it tighter but you'd better be checking everything on a regular basis...
If your looking at an engine that has higher compression & a big cam which = real tight piston to valve clearance you should check every cylinder... If your running something in the 540 lift or less checking one hole is probably fine...