I have mine in a boot bag, which I pack at one end of my holdall. Then I stuff the boots with any fragile stuff - my GHDs fit in one beautifully! So does my makeup bag. I also pack stuff like undies, socks, gloves, etc in the bootbag around the boots. Then I fill up the holdall with the rest of my stuff.
If you check them in separately, it's one more thing to wait for at the other end.