You could hire one of the channel developers here to write your server code for your linking process. Without knowing more specifics about your integration it'd be difficult to give you direction that you'd be completely satisfied with.
To expand on that, you'll want to be sure you have some kind of webserver installed on your linux server machine, probably with php or asp, and some kind of database to store what you need for quick reference lookups like SQL or MySQL.
All the Roku does is either generate a code, or ask your server for a code, and the server would have a way to check the code is valid and link the roku to a user ID, and then return a value to roku so it knows it's been linked. It's probably difficult to do the first time, but once you have that working the rest of the queries (search, billing, viewing logs, mailing out free T-SHIRTS, etc etc) is fairly easy.