Can't say I've done it, but as Ken pointed out, you should be able to assign the Remote Agents as User-Defined Selections in your backup jobs.
So while editing your backup job, go to Source>Selections, then right mouse on User-defined Selections and choose User-defined Selections.... Now add a UNC Name of something like \\192.168.1.24 or whatever your Remote Agent running server is assigned to and click Add. It'll talk to the server at that address and try and communicate with the Remote Agent. If all goes well (and you're routing is working correctly) then you should be able to expand the selection list out and see your server there ready for file selection.
Also check the Network and Firewall properties on the job, as it allows you to pick which Network Interface you want to be using for backups. Pick the one for your VLAN. There is some info in the Backup Exec 10 help under the heading 'Changing the Backup Network for a Job '