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In most cases, authentication for CWP is done via a single user (EG CWPuser) account, this is so you can statically store the connection info in a single file that is then used universally for access on your site.
Adding user authentication for per user would require a lot more complex development.
A middle-of-the-road alternative would be to use a single account for authentication, but then have table based user account management on the filemaker side, so you could query the accounts table and use it. Darren's Accounts module is a good demonstration of that:
For CWP purposes, the account connection is purely transactional (meaning it's only "connected" when the web application is sending or receiving data, otherwise disconnected). But to answer your question directly, yes, the user will be able to connect using two different methods and the same account; BUT, they will count as two connected users, at least for the brief instance that CWP connects.
Great, thanks Mike. Very helpful response!