should I pre-stain the panels in a frame and panel headboard?

YES! always

-- Doug...

Yes, I would. Just be sure to dry well before installing.
Some even just stain the edges and finish the rest when its time to finish the whole piece.

-- I don't make mistakes, I have great learning lessons, Greg

I agree, Im not sure if you use birch plywood often but I would use a pre-stain wood conditioner on the plywood, it will prevent blotching and makes a world of difference in the finish, at least that has been my experience.

-- Salem, New York "Find something you love to do and you will never have to work another day of your life"

I do like to stain and seal the panels before they are installed. It just makes for cleaner finishing later. You don’t say how wide your rails are, but there shouldn’t be alot of movement. The bigger concern would be if you were using solid wood panels. I would think a 1/32 space on each edge of the panel would be plenty. You may want to use something to cushion the panel in the rabbet so that it does not rattle.

-- Lynn "If you think you can do a thing or think you can't do a thing, you're right". Henry Ford