(You can slip a bead on a crochet hook, and then hook the st off the needle, slip the bead onto the st, and replace the stitch on the needle.) Exactly how I do it. The setback for this is that the hole in the bead has to be large enough for the hook to pass through.
You can take a separated strand of yarn and thread them onto it as well. It is tedious....remember that the expensive pre-beaded stuff is that costly for this very reason. I don't think they do it by hand and it's probably done with the bead only on one or several strands. They are also done randomly and to assimulate the pre-beaded yarn, you'd need to do the same thing.
Another option is to knit the entire garment, then randomly sew beads on with a small beading needle and some very strong thread. Beading needles are very sharp and long, allowing you to put very small beads onto the garment. Quilting thread is the best, reliable choice, but is thick and might not thread into the beading needle eye. Silk thread is another good choice, silk being extremely strong. It will be tedious but will turn out very nicely. Good luck! Hope you go for it and I'd love to see it finished! Mary