I don't know about all the marks you're talking about, but if you're talking about the ones on the crankshaft pulley, they are timing marks that are a certain degree of timing each. There is a point on the block that you gauge the marks with.

I'm not positive which mark is what on your engine. It's been a couple of years since I've toyed with Honda engine timing. I Googled "d16y7 timing," and I sourced this out for you:

http://www.c-speedracing.com/howto/timing/timing.php