I haven't made the shawl pattern you are looking at but I have added beads to my knitting. I like to add my beads as I knit as opposed to pre-stringing them. I use a very tiny crochet hook, load the bead on the hook and then with the hook, pull the loop of the stitch I want the bead to sit on through the bead.
Here's a good explanation of the process:
Beading Made Easy!
When you get to the one stitch that replaces your bobble, you would pull the loop of the knit stitch through the bead, replace it on the left needle and then knit it off.
Good luck on your shawl project!