Mine are young as well, and they really can't work independently right now. But it's also too much for them to simply work straight through their schoolwork for the day start to finish. So, this is what we do:
Beyond kid does math & LA, then takes a break.
LHTH kid does math (he wanted more so we've added in a math book for him), fine motor skills, then gets a break.
Beyond kid does history and rotating box, then break.
LHTH kid has Bible box and does his finger play, break.
Beyond kid does poetry and Bible and music, then break.
LHTH kid does letter activity box and Bible Activity and music, then break.
Beyond kid does story time and reading boxes, then she's done.
LHTH kid works with me on phonics (The Reading Lesson) and maybe a page of Explode the Code (not part of HOD, but he loves the books), and then he's done.
Basically I do a couple of boxes and then switch to the other kid. If I try to make them do everything at once, they get completely burnt out. It's a simple system, and it works slick

It does still take up most of our morning, though. Which is actually very good, because in my house, 3 kids under 6 with nothing to do = trouble!

HTH a little bit.