This is from the current Emo manual for their amps on page 29. I couldn't find anything else in the manual which would preclude a power conditioner being installed. The manual actually suggests installing a line conditioner in some cases. It assumes that the conditioner will be sized to provide sufficient power to the amp. I would hate to see you lose your amp due to lightning, even though it does have installed protection devices.
Turn on and Turn off Thumps
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Plug the amplifier into an unswitched AC outlet, and use the 3.5mm Trigger Input connection with a trigger between 5-12 VDC from the source unit or preamplifier. This should allow the amplifier to turn on and off silently.
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If your powered subwoofer is the cause of the “thump” sound (not the other speakers connected to the amplifier), plug it into a different 115VAC outlet than the amplifier so there is no power surge conflict.
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Install a line conditioning device.
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Music system
Model 990/7500/Magnepan 1.6 QRs/Technics SL1200 MK2/Aperion S-12 Subwoofer/OWA3/Sony NS75H DVD
APC H15 Power Conditioner
TV System
Large Advent Loudspeakers/ Polk center/Monoprice surrounds/Panasonic Viera 42 inch/Onkyo HT-RC260/Sony BDP S590/Directv
Home Theater System
Onkyo PR-SC886/Outlaw 7125 Klipsch RF-82 L/R,RC-62 center, RB-35 SR/SL, BENQ HT1075, Outlaw LFM1-EX/OPPO BDP-83/Directv
Harmony ONE
Blue Jeans and Monoprice interconnects
APC H15 Power Conditioner