This is a feature in the BIOS of the motherboard you are using. You typically have to access the bios (usually F2 or ESC, for example) and then enable VT-x.
Unless I am misunderstanding your question... What board are you using?
Your question may be better addressed in the Forum: Embedded Community |Embedded Community
I'm currently using eval board from Congatec (Board name Conga-B7XD). It uses Intel XeonD family processor capable of VT-x. With this board, I suppose I could use the function-key/ESC sequence to configure/enable it. However, this reference design would become part of our production. I'm thinking how it may look like there, and am trying to avoid having to manually configure every chip/board the same way.
I'll try the Embedded forum you suggested also. Thanks.