The side with the spring will go into the engine. Be sure to position the weep hole at 12 o'clock if you've got one to help air escape.
Also, I've found that using a thermostat gasket with glue on one side will help keep the thermostat in the housing when you line it up to the intake. An alternative to the sticky gasket is using some tacky gasket maker.
Good luck, be sure to "burp" the system, you can search out the process on here but the jist of it is to start the car with the radiator cap off and (CAREFULLY) squeeze the upper radiator hose to get the trapped air out of it!
Wes