Hi Cassidy,
ArcGIS Enteprise Builder is meant to enable the easily installation of the Web GIS pattern (e.g., Portal for ArcGIS + ArcGIS Server + ArcGIS Data Store + associated Web Adaptors) on a single machine, it is not designed, nor meant to be used to upgrade an existing ArcGIS Server site.
FYI, What is the ArcGIS Enterprise Builder?—Documentation | ArcGIS Enterprise
> Second question, will both Server(Enterprise?) machines utilize the same Portal installation or will they each have their own instance of Portal as well? Right now they act as production and publication servers but are not linked into a single site.
This depends on what you want to deploy. Right now, the two machines serve as a production and publication site - in which case, you could keep this type of deployment and install a Web GIS on each machine. So you would have 2 Portals. Or, you could keep a Server site on each machine and have them both work with a single Portal - but then you would not have a production and publication environment. It is entirely up to you.
Hope this helps,