It sounds like you have an early type set of neg plate carriers. The later ones are both black, I have both types.
Generally I would suggest that you use the plate with the four studs on the bottom, the idea is that you can slide the film inbetween the rivets/studs and within reason these studs centralise the film.
I find this is not quite the case, but very nearly so. I hold the film in place with a bit of removable Magic Tape. This tape does not leave any noticeable residue on film and pulls easily and cleanly off.
The top plate has four holes and you may find that there is a recessed area around the frame hole on one side. That recess, should face you light source. The idea is that you have a slimmer vertical edge for light to flare off, so eliminating as much as possible, degradation of your print.
Once you have the plates in and with the holder closed, check that plates are perfectly aligned, I normally find that left to right there is enough play to have the plates out by about a millimetre, simply placing you fingers inside and forcing (easy) the plates to align, takes a second or two.
Fore and aft alignment is another matter, I have to put some small paper shims in one end on the holder where the plates wedge in, this brings one plate forward about .5mm then both plates on my holder, are perfectly aligned.
The neg hole is exactly correct for a full frame 24x36mm negative, getting the plates aligned is simple, and makes life really easy.
Mick.