Well, technically the "flywheel" in your case is a "flexplate".
The critical issue in what you are doing is to make sure that the torque converter is fully seated in the front of the transmission as the torque converter has to lock into the front pump of the transmission and be fully seated or the torque converter, or the transmission, or both will be damaged during assembly to the engine.
IF the torque converter is fully seated then all you have to do is rotate things until the flexplate and torque converter line up. This is best accomplished with the spark plugs removed from the engine, then you can use a pry bar in the "teeth" of the flexplate to rotate the engine (much easier to do when there is no compression) until things line up.
Good luck.