Once your clear adhesive is dry, take your scissors and just cut the excess paper away from the pebble. Don't worry about being fancy, who looks at the back of a magnet?
Note: if you want the backs to look fancy, you should go ahead and use a file to file the excess paper away. But it takes way longer. I'm just saying....
After that, place a dollop of strong adhesive on the back of the paper, in the center-ish of the pebble. Don't worry about being exact.
Okay, now, if you want this to be waterproof, or are going to make a necklace or coaster or mosaic or some such, go ahead and seal the entire back of the collage with your epoxy. I reccomend the E6000 clear. It is super stinky, but awesome. If you are just going with the magnet plan, you can skip that part.
Time to grab your magnet. Go ahead and press the magnet into the adhesive. I like to swirl mine around a little, to help center it, and also make sure the whole magnet gets adhesive on it. And now, the hardest part.... waiting for your glue to dry... again.
Here is a try of finished pebbles, awaiting their future home on some magnetic surface.