Intake swap

I need to check a few things first before I go ahead and swap intakes. Once the heads have been cleaned and free of grease etc, I apply gasket sealer to the head as well as the one side of the gasket. After placing the gasket do I then apply the silcone around the water passages? Or should some be put on before the gasket? I have been told NOT to use the cork end gaskets, so I won't but I have some permatex black. Now this is what I was going to put along the water passages as well as the front and rear where the cork should go. What are the risks of using to much in these areas? How do you know it has a good seal? How long do you guy's wait before placing the new intake? And should I use the Permatex black on the intake bolts as well?
It has been years/decades since I have done this, just want to make sure I have all the steps right LOL.
Why do most say not to use the cork end gaskets.
Sorry about all the questions, but I know you guy's don't mind LOL
Thanks
AL