Hauptwerk doesn't currently have support for sample files with more than two channels (surround formats), although we do plan to add support for that natively within Hauptwerk in the future.
In the meantime, sample sets that have surround support do so by having multiple sets of stereo samples (a stereo pair for 'front/close/organ' and another stereo pair for 'rear/diffuse/church', for example), with the various stereo positions being implemented as separate ranks/pipes in Hauptwerk (but which sound simultaneously from the same stops). The user will then see the various positions as separate 'ranks' on the 'Organ | Load organ, adjusting rank audio/memory options/routing' screen and may thus choose whether to load all positions (or just a subset, such as 'front' ranks), and to which sets of (stereo) outputs/speakers he/she wishes to route them.
If you haven't already done so, I'd recommend having a look at any of the existing 'surround' sample sets for Hauptwerk. (E.g. amongst Milan Digital Audio's sample sets, the Metz St. Eucaire is implemented that way.) Some of the surround sample sets from other producers have cut-down demo versions available for download from producers' websites.