My previous attempts at beaded yarns have tended to sag. The completed yarn had droopy loops with beads flopping everywhere. Both knitting needles and crochet hooks tend to catch in these yarns. I wanted to bead yarns in a way that trapped the bead (or pompon, or charm) in a way that kept add-ins from sliding and kept the yarn from stretching.
If you don't know how to Navajo ply, there are many great tutorials on the internet. I won't bother adding one. If you know how, it's easy to add beads to your chained single.
You'll need a tiny crochet hook. The beads will need to fit over the throat of the hook.
Get your yarn started plying. I leave the last few yards unbeaded for tying the skein and for casting on/swatching. I don't like wasting beads or my time.
After several "chains" pull a loop 4-6 inches in length through your working loop. Keep the twist pinched awaying from your working yarn with your nondominant hand.
Put a bead onto your hook and push it back to the throat.
Catch the tip of your working loop with the crochet hook and slide the bead down the loop.
Spread the loop open again and continue chaining (Navajo plying) your single, adding beads as often as you like. I added a single glass Blue Moon bead every yard or so for this 100 yard skein.