When Bunnyshell adds an application it adds the virtual host/server, the application user/sftp user and configures a separate fpm pool for the application.
The php binaries are shared across the system so switching the version is a matter of creating a fpm pool and changing the server to use the specified pool. We support managing the configurations for both nginx and php fpm and it is making it easy by providing templates for it but we are planning to support change php version as a single click. In order to force all applications to be configured with nginx you can create the virtual machine and install nginx with bunnyshell prior to adding applications.