Maximum PC

If building a new system using a motherboard with no video onboard and using a good video card, does the HD graphics in the cpu really matter?

Technically, the wording of "onboard video" for motherboards is a bit misleading now days since a number of modern cpu's now include a gpu core. It's still considered "onboard graphics" even though there's no actual graphics chip on the motherboard itelf, but supports the outputs.

And no, it doesn't unless you are talking about AMD and using their async crossfire that pairs the cpu graphics with a discrete low end card for better performance. It usually disables the cpu graphics in most other instances.