I removed the head on my civic, but all I did to take the timing belt off the cam gear was loosen the adjuster bolt so that I could slide it off. Well after I put it back together and spun the crank a few full rotations the timing marks I made did not line back up. Is the okay? Or did I do something wrong?

 

For the moment, ignore the marks you made. Are the cam and crank perfectly synchronized at TDC1?

 

take out your #1 spark plug the one closest to the timing belt side of the engine. and stick something long and skinny down into the spark plug whole. now go with a 17mm sock and ratchet turn the engine until the tube u put into the spark plug whole goes up and when it goes up turn the crank until the tube u put in the hole is all the way up. pretty much the piston has to be all the way up on top. that's the blocks TDC setting. Now look at your camshaft sprocket. does it say TOP on the top of the sprocket? if not then the timing jumped and the TOP need to be on TOP and the 2 arrows should line up with the valve cover. now put the belt back on and your all set.

 

Let me elaborate, I was in a hurry when I typed the OP.
My motor was burning coolant like mad, so I decided to take the head off, check for warpage and replace the head gasket. Well I didnt want to take off the main crank pulley, so I popped off that little black dust cover that goes over the timing belt tensioner adjuster nut and loosened it. That gave the belt enough slack so that I could slide it off the cam gear. Before I did all this, though, I put the motor at TDC on the compression stroke and used white-out to mark the timing belt and cam gear. Anyways, after I was done with the head gasket, I slid the timing belt back on the cam gear, making sure to align the marks I had made with the white-out. After that, I spun the crank with a ratchet to feel for resistance. There was none. But the timing marks I had made were not lining back up. Should they be lining back up?

 

Don't worry about your marks. Use the marks Honda put there. If you were in fact at TDC not 180 out.

This is simple if you use the OEM marks. I have done that many times.

Step back, take a deep breath and look at what you have. Worst case, pull the belt back off, line up the OEM marks and try again.

 

I made sure the crank, head were at TDC, on the compression stroke. And I dont feel any resistance when spinning the crank by hand, so the valves are not hitting the pistons.
I think I get it, though. The crank sprocket has a different number of teeth, its smaller too, so it makes sense.

 

I recall something about the white line on the crank pulley lines up with the second mark on the plastic cover. I haven't worked on a D in a year or more.

Check your PM's

 

put the everything at TDC once more and put the belt back on and turn the crank pulley counter clockwise 3 or more teeth. this will tighten the belt to specs. then tighten the 14mm belt tensioner. it shouldn't jump teeth anymore.

 

Is your tensioner tight? If it's loose, it'll jump teeth

Tension the belt properly and it shouldn't jump any teeth. Line crank pulley up with mark on lower timing belt cover, set the cam gear with the up and two marks on side lined up with the head surface (use a ruler) and put the belt on. Then tension it properly