You didn't read the installation instructions...
when you installed the toilet, did you? 'Cuz they clearly show where to put the vented loop.http://www.jabsco.com/prodInfo/overview/37010-0000_ds.pdfIt's only in MANUAL toilets that the vented loop goes between the pump and the bowl. My book unfortunately fails to make that distinction (although the reference to wet/dry valves is a good clue...electric toilets (except for a couple of "conversions" that only replace the pump handle) don't have wet/dry valves), but the right time to question that was when you saw a discrepancy between that and the toilet installation instructions.The intake vented loop for an ELECTRIC toilet has to go between the thru-hull and the pump, with an electric solenoid valve (Jabsco part # 37068-0000) wired to the flush button. The solenoid valve closes to prevent air from being pulled into the line that prevents the pump from priming when the toilet is flushed.It must also be at least 6-8" above waterline AT ANY ANGLE OF HEEL, so 3' above the waterline when the boat is at rest may not be high enough when underway and heeling.However, a vented loop will not prevent water from being forced up a line through an open thru-hull by the pressure of the water against the hull when the boat is underway--an effect known as "ram water"..the only solution for that is: keep the seacock closed except when the head is actually in use.Electric toilets should also be on their own separate dedicated circuit with its own breaker, shared by nothing else--not even cabin lights--that can reduce the voltage to the head if on at the same time...'cuz low voltage to the toilet causes all kinds of problems--sluggish discharge...it'll also gradually burn out the motor.