How do you get the transmission to line up with the engine in a 1986 Chevy?

You didn't say if it was an automatic or a stick shift.

A Chevy engine and Chevy transmission should line up fine (A Buick/Olds/Pontiac transmission won't fit a Chevy engine and vice versa.

Lets cover a couple scenariOS that could cause problems:

If it's an automatic and you bolt the torque converter to the flex plate and try to put the transmission in that way you're in for big problems. The torque converter has 3 things that have to line up and engage in the transmission before you can bolt the transmission to the engine block -- the input shaft splines, the stator support splines, and the front pump drive lugs. You must put the torque converter on/in the transmission and turn it while pushing it into the transmission until all 3 of the above have engaged and the torque converter is all the way in. Failure to do this step right will result in catastrophe. You should be able to line up the transmission with the dowel pins on the back of the engine block and push it by hand all the way until it is seated against the block and still be able to turn the torque converter by hand when this is done properly.

If it's a stick shift the clutch disc needs to be centered with the pilot bushing in the back of the crankshaft, if it isn't you need to loosen the pressure plate and use a line up tool or an old discarded input shaft to line it up, then tighten the pressure plate to spec before putting the transmission in.