If you want to be completely sure first off crank timing gear and cam timing gear (the gears the timing chain run on) have to have marks lined up not only with each other but you should be able to draw a straight line through both gears at their center. In other words, a line from the bottom of the crank gear, through the center of the crank gear, through the crank gear mark, through the cam gear mark and through the dead center of the cam gear. If all these marks aren't in a straight line, something is wrong.
To check for TDC, rotate the engine while holding your thumb over #1 spark plug hole. When a) your thumb feels pressure and b) BOTH intake and exhaust valve are CLOSED completely on #1, that's very close to TDC. If you feel pressure but one of the valves are open, you are on the exhaust stroke, not the intake stroke.
If you want to dial in TDC very accurately, you have to buy a tool that measures the height of the piston in #1 as it rises. It's a floating device that fits into #1 spark plug hole and tells you exactly when the piston is at its very top. Knowing this, you can mark your crankshaft damper.
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