The stacking order of the boards would have been obvious once you installed the pots. Since this might be your first PedalPCB build, make sure you install the pots correctly (see below). Some folks get it backwards the first time.
You can get by without an oscilloscope.
If you have a DMM that measures frequency you can use that, or you can just adjust the clock by ear. (which is what I do, despite having a DMM and a scope) I set Depth and Manual to minimum, turn the clock all the way down and then gradually increase until it doesn't sound "robotic".
There are cool sounds outside the range of the Boss service notes, so just go for what sounds good to you.
This is not the Byzantium PCB but the pots are installed the same, just for reference.