We have been in the exact same situation a few years ago as we acquired a smaller company and they had their own domain already, though an older version of Windows. It's just a matter of cross-domain trusting to enable (if your Windows Version are in the proper version of course, AD changed a lot with 2003 or 2008 (can't remember when)). Once the trusted relationship is enabled, it's only a matter of assigned the proper AD user in the GP credentials and open them the access to the web client. If you're not comfortable (or familiar) with the GP setup, you'd probably mandate your partner to do the setup.. Though the actual GP Web server isn't very complicated, it's all about the security certificates that are required to run the GP Web server, and if you screw up there, it will never work.
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