Can the authproxy file be configured to sync AD as well as configured for VmWare View, as part of documentation on this site? I do not want to mess up the config currently in place that sync my DCs.

Yes! Check out our AD Sync instructions:

To configure an existing Authentication Proxy server for directory sync, simply append the [cloud] section of the config file downloaded from the Duo Admin Panel directory properties page to the current authproxy.cfg file located in the Duo Security Authentication Proxy conf folder. Save the configuration file then restart the Duo Authentication Proxy service.

The opposite also holds true, if you’ve already configured the authentication proxy server for AD sync, just append the config sections necessary for VMWare View to the authproxy.cfg file.

Can the Proxy be used to power multiple Duo applications?