I have a linked server and I'm having a tough time referencing it properly.If I open SQL Management Studio and run a query on the server itself it works great.However, I want to take that query ...

That server then breaks down the query (exactly as your server did) and passes whatever SQL it needs to whatever linked servers it has.

A fundamental skill for DBAs is to have a firm understanding of the SQL Server database engine's system databases. Tim Chapman discusses these system databases.

ServerAdmin: Any member can set configuration options on the server. SetupAdmin: Any member can manage linked servers and SQL Server startup options and tasks.