It is not an uncommon practice in NMR spectroscopy to acquire spectra with both positive and negative peaks. The most well known examples are the APT and DEPT experiments. However, to obtain valuable chemical information from them you should first phase these spectra. The standard way around this problem consists of phasing the normal 13 C spectra, remembering the phase values and applying them to the APT or DEPT spectra. This approach is generally used for solvent-suppressed spectra, but due to small phase inconsistencies, does not always work well.
Problems begin when the number of spectra to phase manually number in the hundreds or more.
Generally there exists an exact correspondence between the FIDs' name and the names of the processed spectra. This fact is utilized by the PhasebyFile macro command. However, one should phase it before any further processing. Open the Macro Organizer and press the New button to create a new Macro. The Edit Macro dialog will appear.