There are no guarantees.
It does have a sub-out, but it is not a line-level RCA-out. Rather, it's a speaker-level sub-out. The Pioneer sub that originally came with the unit is passive. However, before I go feeding a speaker-level channel into the Energy E-12, I want to know for certain that I'm not going to damage the sub.
First off, I scoped out the manual on the Energy sub. It's a pretty good sub and offers a lot of setup options to match with virtually any "real" receiver. The sub does not
require an RCA input. It's an option to allow flexibility in fitting into a wide variety of sudio systems, but it does have it's limits, and your receiver is beyond its limits.
Your manual :
http://www.energy-speakers.com/source/ES-12 and ES-12XL.pdf
Unless you have a line-level (RCA) sub output, you have no way to utilize the sub's line-level inputs.
Now, the bad news. Realize that you have a receiver from a HTIB system, which was made to work with a speaker system designed specifically to work with that, and only that, receiver. Forget about using the sub's line-level inputs with that receiver.
Ergo, the receiver's speaker level subwoofer outputs. The receiver does all the thinking and amplification and sends it's output to a "passive", or non-powered subwoofer. This type of HTIB is the lowest level of HT systems because it doesn't lend itself to upgrading. These particular HTIB receivers don't play well with other subwoofers. The odds are that your main speakers are sent a "filtered" output that withholds all bass and diverts it to the sub.
So, now you want to use a "real" powered subwoofer with all the rights, honors, and priveliges this entails. It ain't gonna happen. To work correctly with your receiver, you need a "passive", or non-powered subwoofer, that most likely reproduces higher frequencies than a normal subwoofer. In actuality, it's more of a "bass box" than a subwoofer.
You
might be able connect your receiver's speaker-level sub output to the one of the sub's speaker level inputs (or maybe jumper them together) and, if I were you, I'd stick with that option. Those inputs are made to handle speaker level inputs, which your unit puts out. Crank up the crossover as high as it goes and don't bother connecting your mains to the speaker outputs on the sub. don't be surprised if you lose a some sound in a band of frequencies (the Bose efect) because odds are that passive sub was designed to go up higher than this sub does.
And, if I sound a bit terse, it's because you led us on a wild goose chase. Being in the consulting business, I'm sure you are aware that when a customer doesn't provide all the facts up front, troubleshooting can be hell. But, if you charge for the hour that can be a boon. We offer advice for free here.
That sub can, in fact, accept speaker level inputs with ease, as the link to your manual states. That, and you neglected to mention up-front that your "receiver" had speaker-level sub output, which is very, very rare. Virtually all "real" receivers use line-level subwoofer outputs and that's the assumption we work on, unless told otherwise.