If you're using docker (which you should) there's really very little value (and quite a bit of cost, resource wise) to putting everything in separate VMs.
Edit to add: for KVM/QEMU, you're probably best off just using Proxmox as your host OS. If you'd prefer not to do that then the easiest way to manage QEMU is with virt-manager, either connecting over SSH, or piped from the host using X forwarding.
I'm a big fan of KVM/QEMU, I use it at work and at home, but it does have its quirks, so prepare for a bit of a learning curve.