Hillbilly method (been awhile since Ive done it this way so bear with me.)
Pull the plugs and flywheel cover.
Take a pencil and put it in plug hole
Rotate flywheel by hand until you see the pencil at TDC... (roll in back and fourth a few times)
WITHOUT MOVING FLYWHEEL move pencil to opposite plug hole.
Rotate the flywheel in the SAME direction you were rotating and see if the pencil drops.
If it drops that means that you have one cyld at TDC, and one that is not at BDC... If it raises that means that one is at TDC and one is at BDC. Now this isnt a scientific way to do this, but its been my experience that when they vibrate like you are saying they are far enough out that you will see it pretty clearly. Its a cheap/easy way to give it an initial look.