Welcome to Nitro. You will love it if you're patient
"this is my first time dealing with a non-pull start engine.
i have a starter box and all, just don't know how to start the engine. i read somewhere that the starter box should rotate clockwise while the flywheel turns counter-clockwise."
Yes, the flywheel goes counter clockwise and the starter box wheel goes clockwise. Just make sure the car is aligned with the box. Make sure the middle of the flywheel contacts the middle of the starter box wheel.
"my ignitor is working. is there a way to prime the motor?"
A way to prime the engine is to plug the exhaust stinger hole.
Another way is to take off the pressure line connected to the pipe and blow on it. This is a bit dangerous since you might suck up some nitro.
"also my concern is, when i place the flywheel on the starter box and push down to make contact with the starter boxes rotating wheel. the motor seizes up at the top/bottom stroke. i can't get the motor to turn over."
An easier way to turn over the engine when the engine is hard to start is to heat the engine up with a hair dryer or heat gun, to expand the metal inside.
Hope this helps