It depends on the situation:
If SONAR is reporting them "missing" on opening the project, you just need to select the "Move" or "Copy" option in the dialog after telling it where to find the missing files.
If, on the other hand, the project is correctly referencing the files but they're not where you want them, you can manually move them from the currently referenced location to the project's Audio folder (with the project closed), and choose the "Reference" option with the new location when SONAR reports them missing from the old location on opening the project.