Markers can now be set across multiple marker sets using the 4th line on signs. I've also done quite a bit of code cleanup, so things should act a little bit more "normal"
If you're upgrading the 1.2 I highly recommend editing your markers.yml in the BleMap web folder to prefix both the NAME and ID of the default marker set for BlueMap-Signs with bmSigns_ so that it knows to use it instead of creating a new one! If you need any help figuring that out, just ask <3
You can see how to use and manage Marker Sets within BlueMap-Signs on these wiki pages.
New commands and permisions
Marker Set information