I can’t promise you the way I installed the seals is correct, but I can tell you that we have gone over 4000 miles since installation with zero water intrusion. The way you received the seals fitted together is not the way they are installed. Also, the seals will not be flush, but will be about 1/8” above the flat surface around them. Because of this, I attempted to contact cement the upper foam seal against the silicone seal, and that didn’t really work. I now have the foam seal free floating between the bottom of the motor and the top of the seal. It really just acts as a pad between the motor and the seals when the motor is in the down position. You do not need the foam seal to prevent water intrusion, as no water gets by the silicone seals. Another difference in the install is that I used a lot of adhesive RTV sealant (black) to firmly hold the seals in place, and have had no issues with the seals coming out. I also put a very thin coat on Moly-kote on the shaft of the thruster to make it move a bit easier through the 2 seals. see the attached picture for the orientation of my seals.
Prior to the installation of the silicone seals, we always had water getting in the boat in spite of servicing the thruster once a year. This is one of the better improvements I have made to the boat, and it has completely solved the water getting by the seals issue. Another benefit is that I see absolutely no reason to change the seals until you see some deterioration of the silicone, which I expect to be many years.
Good luck with the install.
Aloha SM 72
Anchored in Poulsbo, WA