You can change the super tool mode by sneak+right clicking while you are not pointing at any blocks. Point towards the sky or off into the distance.
There are 3 different modes:
Mine: mines blocks in a 3x3 area.
Build: places blocks in a 3x3 area. Click on the side of a block to build vertically and click on the top of a block to build horizontally.
Fill: similar to build but only replaces existent blocks with the block assigned to the tool.
To assign a block to the super tool, right click on the desired block while sneaking.