Install it before the transfer switch. Not sure about the instructions you have; instructions with mine cautioned against installing after the transfer switch and said it wouldn't work that way. I took the advice of another post and made the install where it could be removed easily, too. Bought two 50A range cords and two 50A receptacles. Put one receptacle on the end of the shore cord, then put a range cord on the power in side of the EMS. On the power our side, I put the other receptacle, then installed the second range cord to the power in side of the transfer switch. Just plug it all together and you're set, but you can remove it and connect the shore cord directly yo the transfer switch if needed. Also, this arrangement ensures nothing that's hot is exposed to shock you.
2015 Legacy SR340 360RB
2014 Jeep Wrangler Unlimited Toad
Gigi, Poppy and Sadie Lady...On the road, but not full time!