The info on yamaha's music cast is poor as well and the online manual is not a heck of a lot better. The music cast app has some bass management features. You can't set the cross over but you can set the volume and you have to pick the "size" of the speaker (floorstander, bookshelf, compact, etc.). I have no idea what that does to the crossover within the amp but it has an obvious impact on the signal going to the speakers and that will have an impact on how you set the crossover on the sub.
When I bought my yammy preamp (WXC 50),I almost returned the damn thing because the SQ was so poor with my floorstanders until I figured out that there was a setting (buried deep, deep within the app) for speaker type.