if it is TDC, stick a small screw driver, or straw or something that can hit the piston down the spark plug hole, and when you hand roll the engine over, the piston will reach the top of the cylinder. TDC is when the piston reaches the top of the cylinder. If your engine is TDC, the UP word on the timing wheel on the head will be straight up, and there will be two - - that line up where the valve cover mounts on the head. and you already know about the bottom ||| | are on the crank pulley is, so when its TDC, check all of your marks, and if they are off, then that means your timing is off.
im not sure what engine you have, and i dont really feel like going to page 1, but i have a D15b7. I think the D15b7 and B15b8 both have the same timing method, but if you have a different engine let me know and i'll post some of the civic manual pages on where the TDC marks are on different engines,
good luck
Brandon