So it's a box about the size of a small MXR pedal with a 1/4" stereo jack that splits into two mono 1/4" inch jacks. The cables used with the box are one stereo 1/4" cable that plugs into the guitar, and two 1/4" mono cables that plug into the input and output of the effects chain.
The reasons to use the junction box is:
1) Don't need to make special Y-cables.
2) Don't need to plug and unplug cables into effects for each setup and tear-down.
Any other reasons to use a junction box?