At this point and time, sounds like you don't have a choice. Regardless of the age, you have to do something or you will end up with more of a problem. Just watch their eyes and mouth. Although you had separated them the new chicks, I would separate again at this point and remain separated for 30 days.
Do you think the DE is enough? Eyes and mouth is where the mites congregate? Should I go to towels under the chicks or stick with the shavings? Thanks!
Sure, you can start off with DE. I'm not a big of shavings, so you may not want my opinion on those shavings. I use towels but that's just me. Others love shavings but I don't. Shavings scare me. I would sprinkle DE on the floor (shavings or towels or whatever you decide to use). Yes, you will have to get those areas but be careful. How many will you have to dust?