No, that's not necessary. Air will find its way and sort itself.

Like you, I also thought that airflow would be improved by exposing the intake runners to a large pipe - much like the original upper intake - or like a turbo setup - but after trying to find a place to mount the blower alongside the engine, I realized that the top of the lower intake was about the only solution that still allowed me to keep power steering and A/C. That solution also made it much easier to provide a drive belt for the blower.

The choice is yours, but the top location works just fine.

Frank