@evomotors Unfortunately it's a limitation of the current configuration tool. Updating the tool to allow configuration of multiple motors per axis is on our work list, so will happen, just not sure when.
Until then, yes, manually updating your config.g is the way to add drive mapping for multiple motors and leadscrew positions. It's good to become familiar with the gcodes, config.g and other files in the sys folder, so you can further customise your machine beyond what can be achieved with the configuration tool.
Ian