I also use Veracrypt both disk and containers.
Yeah Clonzilla can only clone inactive disks.. and is run in a Linux environment so when on windows, you have two options.. Boot in to the live USB.. OR.. set up a VM with Live-clonezilla or any Linux distro and clonezilla.. But when running in a VM you can't backup the system disk.. But as you talked about working with external drives.. Then a VM should work.. I have not tried that solution as i run linux as main system.
If you use Clonzilla to backup encrypted disk like Veracrypt that is shown as "Raw" Then a sector by sector cloning is needed if you dont want to decrypt the disk.. Just keep in mind if the disk is 2TB and stored information is only 100GB then the image will become 2TB in size when cloning sector by sector..
a nice workaround is to make containers on that data you want to backup.. So if you have 100GB of information on the 2TB disk.. Make an encrypted container of 110GB that you put the 100GB data in.. then you backup the container file.
I'm on my second cup of coffee, so i have not totally woken up yet. *lol*