The vCenter Server Appliance is deployed as a separate virtual machine, and - in case you go with the 6.5 Update 1 version - provides an option to migrate your existing vCenter Server 6.0, i.e. take over the settings (assuming that it is a dedicate Windows Server for vCenter, i.e. no other services running on it). The vCSA can be downloaded from the VMware download section, likely the same location from where you downloaded the Windows installer.
The installation image you downloaded can be used to install, or upgrade vCenter Server. Whether you can install it on an existing server depends on what's already running on this server, and whether it meets the prerequisites (see Installation Guide). I'd suggest that in case you want to use the Windows version, that you use a dedicated Windows Server for it.
André