Need Help setting up sub w/ maggies

Yes, the amp will be driving both sub and speakers. 
The sub will be amplifying the signal with its' amplifier.
Is it the best way? It depends.
My office uses subs connected as you are instructed with the ML's.
So, my amp is running both speakers and subs with full frequency. The bad part is that a lot of power is needed to reproduce lower frequencies. So, your amp is essentially powering speakers and subs with the same signal for 2 different units-which may tax it.

My main stereo uses Vandersteen subs, which use a high pass filter.
This cuts off the low frequencies for my speakers, so they don't need to reproduce those frequencies, and my amp isn't required to output them as well- so lower power demands on the amp.
The Vandy sub is configured to compensate for the diminished signal and then properly amplify via the internal amplifier. 
I am sure others can describe this better, but I HTH.
Bob

This sub also runs a high pass filter when using speaker inputs, so idon't think it'll be a problem, but thanks for confirming that that is how it should/could be done. 

Subs offering a high-level input (from the output taps of the loudspeaker’s power amp) intentionally have a very, very high input impedance on their plate amp. This allows the sub to receive the signal from the amp, but without the speaker’s power amp powering the sub itself. REL and Rythmik are designed this way.