The Yamaha Motif XS and XF formats are very similar, but not compatible with each other...
The 'waveforms' file contains 'Yamaha waveforms', which is basically a key and velocity to waveform map, much like an instrument in Awave Studio, but with the restrictions that overlapping regions aren't allowed. When opening one of these files, each waveform therein will show up as an instrument. When saving, you can save an entire collection, or a single instrument, layer or region and 'Yamaha waveforms' will be created from these. However, for instruments which use multi-layering, only non-overlapping regions will be used. Regions in lower numbered layers have priority over regions in higher numbered layers, and any colliding regions in the higher numbered regions are simply skipped. You will get a warning message if one or more regions have to be skipped.
The 'voices' file contains one or more 'Yamaha voices' (in addition to waveforms) which basically correspond to the instruments in Awave Studio. These include articulation data. Unlike the previously described file type, you should be able to load up a voice directly and play it on the synth. When you load one of these files, the voices will of course appear as instruments and similarly when writing them, each instrument will become a Yamaha voice. A number of Yamaha waveforms will also be created as necessary and stored in the file - each voice can use up to 8 'elements' which each use one Yamaha waveform. This means that the maximum 'depth' of multi-layering of sounds is 8.
The 'all' files can contain many different types of data; voices, waveforms, performances, sequences et c - but only the waveforms and voices are read.