When I did my timing belt the pulley's and the crank shaft gear were all lined up correctly before I took the old belt off. The marks on the belt did not line up with the marks on either the pulley's/gear or the heads/block. I'm sure that if I had turned the motor over enough by hand, then eventually everything would have lined up, but following Bart's (nfpgasmask) instructions I made sure that all of the notches on the pulley's lined up with the marks on the heads, and the notch on the crank gear lined up with the mark on the block. When I took the old belt off, the cams snapped out of alignment as expected. The marks on the new belt are to make sure that everything is lined up correctly when you put it all back together. If you align the marks on the belt with the notches in the cam pulley's and the marks on the heads, and the mark on the belt with the mark on the crank gear and the block, then when you pull the pin on the belt tensioner everything should be timed correctly and the engine should fire right up once everything is put back together.

I wasn't sure if you had a new belt with the marks on it already. If you do then you should be fine, but if you don't, counting the teeth between the marks would allow you to mark up your new belt for easier installation.