Go into a custom game or practice mode to test:
In champ select, click on the dropdown menu for runes and pick one of your pages (prob the ones without the cheezy "The Collosus" names).
They may be simply named "page 1" and "page 2" or you might need to click "create new page."
Then click on the pencil/writing thing beside it that says "edit."
That should expand the page so you can see all the runes.
Click on a rune to swap it. If you want to change the keystone, click the keystone. If you want to change the Path (like sorcery to domination or to resolve ect. Then click the button above the keystone to do that.