Each route into the VPN has its own flow, so you have configured the admin flow for the portal, you should have a LogonBox VPN Client flow which defines the authentication for LogonBox clients.
Attach Duo to this flow and when a client logs in they should be prompted to complete Duo authentication.
The authentication flow can be configured right down to the user level by using the "Assigned Flow" authentication module.
First, create an Authentication Flow for each type of authentication you want to support. Add the modules necersary to each flow, then in the main LogonBox VPN Client flow, or other system flow, add the "Assigned Flow" module.
This allows you to specify any number of mappings of User/Group/Role to an Authentication Flow and provide a fallback/default.
If you don't see the Assigned Flow, your likely not on the latest version as it was only recently introduced.