The probe needs to be on the inside of the enclosure. The temps will go up a little when you add substrate but you shouldn't be using more than 1" deep of it anyways. Also your snake will likely push substrate around to lie as close to the heat source as possible especially after feeding, so that's why you don't want the probe on top of the substrate but under it. If it's on top of the pad between the heat and the glass above you have no idea what your actual hot spot temp is.

Your thermometer probe cord should have come with a twisty tie. Once you secure the probe and have the actual thermometer in place, just fold the cord back up, secure with the tie, and cover it how you wish. You might want to wrap the loose ends back about the 'body' of the tied cord just to help reduce the risk of your snake harming itself somehow. They're not the smartest box of rocks around so it's your job to make sure they don't get a chance to hurt themself. If they do, then it's off to the vet and that's stressful for everybody.