Until now I have created and used Mbtiles from a single source (OpenSeaMap) and this is working very well on my Android devices and my Windows PC.
I have now created Mbtiles from Google Earth and from Bing maps but I find no easy way to switch Mbtiles from one source to another (beside placing the Mbtiles in separate directories and abling/disabling the directories in the settings).
No, you didn't miss anything. There is no way to select easily what set of mbtiles to display, or to overlay them with some transparency.
You are not the first one to ask, it's in the todo list... for later.