If you did not put all the boards on the house yet, paint the tongue
and the grooves first. *That will prevent some rotting when water gets
in them, and it will.

No doubt. I'm cutting off the bottom 20" and putting up new because
it sucked up water and rotted. I'm fully staining the pieces before
they go on and am covering the edges and tongue/grooves. I'll stain
the new cut edge on the house too before I put up the flashing.

I don't think the panels on the house were edge stained. And I know
the panels on the house weren't installed correctly so that they have
some space between the flashing and the edge. That's where the siding
is it's worst.