I think I do the same as you describe
1 - Install the cap and main seal, with the lip facing the right direction, torque it
2 - Fit the side seal so it goes in very easy but some resistance.
FYI - With Felpro seals, the side seals and nails are HORRIBLE, they are hard, the nail is sharp, so I don't use them anymore. Mahle or Victor (same) are soft and a blunt nail, and so far have not needed any sanding
3 - Push a good amount of RTV into the hole, I like the Black Ultra for heavy oil environments
4 - Coat the side seal, push it in and it squirts out, get it all the way in, usually ends up flush, if it doesn't I have a punch that I used to push it in
5 - Drive the nail in, in the groove, being careful not to damage the side seal (This is where Felpros fail, the nail cuts into the side seal and then binds, damages, you name it. Junk.... At this point, the side seal is about 1/8-3/16 below the pan surface
6 - Clean up the RTV that pushed into the engine well and on the pan rail
7 - When you are ready for the pan, put a dab in each side seal at the top
Knock on wood, haven't had a leaker in a LONG time
I see Brent use some good stuff and just squirt down the hole, it works, I can't say a single bad thing about the stuff he uses. He will likely chime in on the sealant he uses to do that