Yes the mark will be on the tooth of one gear and the valley of the other gear. When #1 and #6 are at TDC, either 1 or 6 will be ready to fire and the other will be ready to start the intake cycle. However, the timing marks are the only true way of timing it properly.
I would try and use a rope seal on a 54. If your mains have shims, I would adjust all of them. If they are sloppy the rear main will never seal very well. When I finally replaced my mains my new seal worked perfectly.
