These types of agates are usually really transparent, and I can't
picture how any glue would not show through badly.
I've done it many times and never had a problem. I use
cyanoacrylate ("super glue"). The only way the glue could show is if
there are gaps; but if the glue takes up all the space between the
back of the stone and the surface it's being glued to, there's no way
it can show.
Let's say I'm gluing a stone onto aluminum foil. I smooth the foil,
squeeze out the glue, use the side of a toothpick to spread it evenly
and place the stone. I don't worry about extra glue getting on the
sides of the stone because when it's all dried, I take an Exacto
knife and shave off any excess. Then I wipe the surface of the stone
with acetone. Also, if the glue is drying too slowly (which it will
do when there's volume), and I'm getting impatient, I'll spray with
an accelerant (I think it's called Zip Kicker). YMMV, of course.