If you get your head directly above the inside lip of the rocker panel, look straight down, and get an inch mark by eyeballing the center of the rocker panel lip, then moving to your left put a little scribe mark at 2" on the rocker panel.

You can see my little scribe marks here.

Then move the pan into position.

Put a couple screws in the lip of the rocker to hold the pan in position. (the picture
I have of the pan in position didn't turn out, so assume the pan is in position)
Now measure 2" from that scribe mark on the flat of the rocker panel and put a scribe 
mark on the floor pan. I took the pan out, laid it on the table, put a couple of 2x4's
under it and drilled this 3/8" hole.
Over to the right you can see the hole I drilled in the pan, it's a 3/8" hole. Then I
put the pan back in position and made a circle with a magic marker on the rocker panel 
flange. This is pretty important about those holes in the pan. If you're 
going to be off center with your hole, make sure it's toward the rocker panel because 
you want to keep that rocker panel flange underneath nice and straight without any welds 
sticking out of it.
If you make a mistake, a dremel tool will clean it up. When you plug weld the supports,
make sure none of the welds are sticking on the edge of the support itself. You want 
nice clean lines on the pans and supports. This is just a quick explanation of how I
did it, I'm sure you can find easier ways to mark them.