I have been doing exactly what you need to do for many years now. My primary reason for doing it is to organize the file structure. Here is what I do:
1 - Create the folder where you would like your SoPC builder system located.
2 - Don't use the little SoPC builder toolbar button to launch SoPC builder. Instead, use the megawizard to create a new SoPC builder system and specify the location of the SoPC builder file.
3 - When you generate your SoPC builder system, SoPC builder will give you an error. It will inform you that the system generated correctly but there were errors. This error can be ignored. The error is generated because SoPC builder wants to add run a TCL script for your Quartus project but there is no project associated with SoPC builder.
4 - Add the folder that contains your SoPC builder system as a user library
Jake