Just as an aside: a QlikView server never connects to the web server or the AccessPoint. Connections typically go the other way. The web server that displays the AccessPoint asks the QVS for a list of documents that should be presented to this particular user, and upon clicking a link or a thulmbnail, forwards the user to the QVS or tunnels all traffic from this user to the QVS where the document is hosted.
A split setup is rather simple and can be figured out from the Help pages here: Upgrade and Migration ‒ QlikView
In essence, you perform two custom installations: one on the IIS machne (where you install the QlikView Settings Service) and another on the actual QlikView Server machine (where you install everything else, except for the QVWS which isn't used anymore). I'm not sure how you can perform an upgrade of an existing system and relocate the web server at the same time. But maybe you better start from a fresh install, or an existing system where you first relocate the 11.20 web server to the IIS machine before performing an upgrade of the two machines to 12.xx. That allows you to test the Migration and Upgrade in phases.