I think you're confused about how to set the firing order. The pistons come to the top of the stroke twice, once at the top of the compression stroke, ready for a spark, and again one turn later, at the top of the exhaust stroke with both valves slightly open. Two cylinders top out at once, #1 and #6. Here's the best way I've found to get it right the first time:
1. Turn the engine, clockwise from the front. Watch the valves on the #6 cylinder.
2. The #6 exhaust valve is the last one in line, right back by the firewall. Turn the engine until it's fully open, with the spring compressed. Keep turning until the exhaust is almost closed and the intake just begins to move. It's the second one in line from the firewall.
3. With the #6 cylinder in this position, called "overlap" or "rocking" THE DISTRIBUTOR ROTOR SHOULD BE POINTED TO THE #1 PLUG WIRE POSITION ON THE DISTRIBUTOR CAP.
4. Start the firing order with the #1 plug wire in the cap position the rotor is pointing toward, and follow with the 5-3-6-2-4 order.
This is the simplest, most foolproof way I've found to make sure the distributor is installed correctly. It's more accurate than trying to stick a thumb over the spark plug hole and look for compression pressure.