Hi James,
If you are using Aperion subs, the best way is to use a Y connector from the low level sub out on your receiver. You can split the low level signal once without any harmful effects.
If you have left and right preouts on your receiver you can also use those for sub out but you will need to be sure your receiver is set up to send a full-range signal to the main speakers through the preout. This can be tricky if you are using booshelf or satellite speakers as mains. If you are using large towers it would work fine.
The speaker level input would be the last choice if the others aren't an option. It requires a lot more wiring but it will work great.
Cheers,
John Wanderscheid