What is the apparent link between pins 1 & 3 and 1 & the rectangular block at the top?
Personally I would have left 2&3 connected in case another device was desired to be connected at any time adhoc. Leaving the iPad in mono is fine or even stereo, signal is going to get there I would have thought, but I am here to learn too.
As for the 1 to 3 and connection to the block at top would avoid those completely.
Using this cable you are clearly using a mic channel input therefore any graphic setting on 5/6 will not apply?
Using a mic channel will give you much easier and faster control over music input volume.
If not the cable you have pictured then a normal stereo mini to two normal jacks might be better, leaving iPad in stereo, using inputs 5/6 and being able to fully employ graphic and limiter / gate and anything else to 5/6 you may want?
Just my thoughts.... and I could be shot down...