Jog levers are used all the time on commercial boats, standard equipment. Many of these operators never touch the hand wheel. A switch should be installed to isolate the jogs when the A/P is in use. Some pilots have a clutch output which can be used to operate an interlock relay. The piggyback circuits will not hurt the A/P but you don't want the possibility of energizing port and stb solenoids at the same time. Of course you want this done by someone with an understanding of it, as incorrect wiring could damage the pilot.
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Experience develops good judgement, bad judgement develops experience