If the round port is no bigger than the square manifold ports, no problem. If the port in the head is larger, it will hurt flow somewhat, though if you're using cast manifolds you can always match them to the head ports with a little work with a carbide burr. Check that the manifold flange and the raised flange around the ports are not mismatched so that there too narrow a sealing surface that will cause them to leak.
Headers will give you more HP and there are many port shapes available.