For the ones with 'stuffing,' I've taken to cleaning them after each use. Although I came up with a great way of telling them apart, it's really just more hassle than it's worth to keep track of which flavor each had/when it was last cleaned/etc. etc. etc. and after cleaning, they'll all take the same amount of
juice, so there's less fiddling.
For CE2s, I refill them as needed
throughout the day and clean them when retiring them for the night.
On both styles, I flush them with 91% Isopropyl alcohol. There are many on this forum who despise using isoalc, and they have many warnings/concerns about using it. I say: 'eh.'

I can't recommend it whole-heartedly, but it works well for me.
I now clean/flush them using a pediatric syringe from Wal-Mart. They're stocked with the baby thermometers, etc. They have a white cone for insertion into medicine bottles but the hole in them is perfect for a carto. I pour some isoalc into a bowl, fit a carto to the cone, and use the syringe to pump the solvent into/out through the carto several times. Then I pump a few more times, without drawing up any isoalc, to blow out the carto. It sounds like a lot of work, but I can do twenty cartos (two days' worth of
vaping) in about fifteen minutes. I let them dry overnight, and they're ready to fill when I need them.
I know there are a number of videos on YouTube, but I don't have the urls handy.