We currently provide a custom nozzle holder for our R&D customers that mounts on the outside of the nozzle block. This began due to the design change between the UM2 and the UM2+. The UM2 still has the hole for a second nozzle, but in the UM2+ it is a solid block, so dropping the tubing through no longer works.
Our custom nozzle mount was designed so that the paste nozzle height can be adjusted, and it can be level with the filament nozzle. Care must still be taken so that paste material doesn't get stuck onto the filament nozzle (this happens sometimes with RTV silicone caulking: it can start getting "chunky" if the local humidity is very high, and these irregularities will then appear as bumps in the surface of the print and cause some material to stick to the filament nozzle).
For the UM2, when we put the tubing through the nozzle block, we simply use a bit of electrical tape around the end of the tubing to make it thicker, so it can be secured properly in the nozzle block.
Outside of these two modifications, the firmware is the other main modification, to enable the second extruder. Gcodes are needed, too, depending on how the print is set up. (If you have the Discov3ry connected on extruder #2, and are only printing with that extruder, then you will need to explicitely include the "T1" command in the top of your gcode.)