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It sounds like the op is running an actively crossed over sub and sending the highs to the tops, and the highs out of it into the ceiling speakers. I would run it this way unless you want bass to come through your ceiling speakers. If you do want bass, then I would run the audio for the ceiling from the mixer. I would look into getting a dsp with an adjustable active crossover for this setup as you will have more fine tuning and better sound than using the subs built in crossover. There is a behringer model that has a hard limiter so you can protect your speakers from the djs who like to push it in the red.
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This- http://www.behringer.com/EN/Products/DCX2496.aspx
The minidsp is a cheaper, more reliable, has better tuning functionality, and is the size of a cigarette pack, but it does not have the hard limiter. http://www.minidsp.com/products/mini...p-balanced-2x4
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I have the unbalanced minidsp for my small rig of two active 12" tops and two passive 18" subs each powered by their own amp. I bought the unbalanced minidsp as I was originally planning on using passive tops as well and the minidsp would have been in the box with the amps under my dj table, but running into ground loop issues (somewhat fixed with a groundloop isolator) I'm planning on getting the balanced minidsp. The balanced version is also capable of handling much louder audio signal (around 2v) for your big rigs.
Another cool thing that you can do is use their usb calibrated mic along with room eq wizard and help get rid of room modes and tune your speakers flat.