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As far as my experience goes kvm is a kernel module and xen must be compiled into the kernel. So you would need a xen-activated kernel and one kernel where you can modprobe the kvm_amd|intel module. When done with this you just boot up the appropriate kernel. Though depending on the bootloader installed there are various ways to do this before the boot or at the boot.
So to answer your question short: You specifiy the hypervisor at boot up.
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