Add the beads individually as you crochet each beaded stitch of your project. For this you will need a teeny tiny steel crochet hook and beads with a large enough hole, or opening, to pull both the doubled up yarn through the hook.
To do this, pull the loop a bit taller than normal. Put a bead on your small hook, grab the yarn and pull it through the bead. Then re-insert the regular crochet hook to complete the stitch.