Tube seal on the left side of pic: center part sits higher than outer, glossy side
Tube seal on the right side of pic: center part sits lower than outer, dull side

I was wondering which side faces up and which side faces down (towards the plugs)

I think the left one faces down, but wanted to be sure (my car had different tube seals in there so I dont know)

And where should I apply some RTV to avoid leaks?

you got it. i put a thin bead of rtv around the whole head just to be sure and no leaks.