Dissolving xylitol in a raw, home-made chocolate
I believe that sugars are usually suspended in chocolate by emulsion - emulsifiers, like soy lecithin, are sometimes commercially used and may improve sugar staying suspended in the chocolate - which may answer part of your problem, if you can find some to try it.  

But I think the real answer to how sugar usually stays suspended in chocolate lies in mechanical emulsion, where sugar is mixed into chocolate and stays suspended in fine particles.  Commercial chocolate does so in the 'conching' stage of chocolate production - where the chocolate is mechanically ground very fine for hours or days, giving a minute particle size to both the cocoa solids and the sugar granules.  

Homemade chocolate using cocoa powder and cocoa butter don't usually need conching, since the solids are already ground to a fine powder - but your xylitol may be slightly coarser and so is apparent in the mixed chocolate as a gritty texture.  Perhaps home chocolate making uses powdered sugar, or the sugar dissolves more easily into the chocolate butter, or in the mouth when tasting, I'm not sure.  I don't think you can add something to make your xylitol dissolve or distribute better, though, as it will probably make the chocolate seize.

You might try grinding your xylitol (with a mortar and pestle, or a spice grinder or what have you) till it becomes a fine powder - if there isn't already a finer grind available, which would be less work. This should also help with settling since the smaller particles will be lighter, although you might need to keep stirring until it's thick enough, or plan to cool quickly enough after it is poured, so that it doesn't have time to settle.