jdaird,
I installed IntelliJacks on my Cougar 299RKS, it works totally fine in conjunction with remote. I disconnected the landing gear switch and tied in the IntelliJacks to these wires. Cougar remote still works to control landing gear, but like you I seldom use remote for landing gear as the IntelliJacks system does all the work. I hope this answers your question, if not let me know, I will be glad to help you out.
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2017 Chevy 1500 LTZ 6.2 Tow Max
2012 Cougar 299 RKS
Curt Q20 with R20 Roller
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