You should use a “datasource” (DB) as your authentication scheme instead of the default “internal” source. You can have FPMI create a basic schema for you or you can explicitly create queries to get the users and roles (groups) from your existing tables.
Alternatively, you can set up Active Directory to get users and groups from your Microsoft Windows Domain.
See the manual under: Gateway->Configuration->Authentication->Datasource.
The system is very flexible in terms of allowing/restricting access to/within your projects based on user permissions (roles).
FPMI is very compatible in terms of integrating with your intranet site. This thread shows URL paths to projects (applet/normal/web start) and the gateway. The various status pages are available as well. You can also create simple single-screen projects that “autologon”, then embed them in your portal as applets or you can launch full web started projects - lots of options.
Beyond authentication, FPMI gateway configuration options are not available externally. You can always provide access to the gateway configuration site from/within your company intranet site.