I have actually yet to try Qubes OS, but am currently looking into testing it. I have not much experience with the dom0 structure - have almost always used KVM/Qemu in the following way:
A debian based core system on a LUKS encrypted root partition and lib-virt which also automatically open and mount my LUKS encrypted partition containing an LVM2 container where all my guest os’es reside. The only part that is not encrypted is a very small boot partition.
Does Qubes support a similar disk encryption scheme, or what is best practices for disk encryption with Qubes?