Oh, I think I get it. Sounds like you're putting it together out of order.
When you start, you should have a chain and two halves of a snap-link. The chain should have two inner-plate ends exposed, so remove half a link if you've got outer plates on one end. Wrap the chain around your cogs, derailleurs, and chainrings the way it should go, then derail the chain from the chainrings so you have some slack to work with.
This is where I think you've gone wrong: insert one side of the snap-link in one end of the chain, and the other side of the snap link on the other end of the chain. Then pull the two ends together, and you can insert both pins into both holes at the same time. Pull, and both pins will seat into both flat parts simultaniously. Put the chain on the chainring, pedal, and it will seat the rest of the way.