If the board is designed with the power LED on the board, they probably have a particular wiring arrangement in mind for the 3PDT. The way I wire my switches up means the board receives power whether the switch is on or off. The switch just controls whether the input goes to the board or direct to output (and it grounds the board output in the bypass position). That probably wouldn't work with your board, since the power LED would likely stay lit regardless of the bypass.
The Pedal Parts Australia 3PDT board has the LED and CLR on the mini board. It might work with your setup just by leaving those out. I have one in my compressor, so I could test if it powers down the main board in the bypass position (assuming that's what your circuit is expecting).
For myself, although I find wiring up the off-board stuff a bit boring, I don't mind too much if it's not perfectly tidy since I am not looking inside the box much anyway. If I was building pedals to sell I would probably put more care into making the box look neat.