A Few Noob Questions

Yes, you are going to want to take the temps on top of the substrate. And this does mean that the heat output of the mat itself will need to be higher than what is being recorded on the surface, because the heat will dissipate when heating the substrate. However, you want to make sure that the heat pad does not get to dangerous levels, due to the snake being able to push aside the substrate and come directly into contact with the glass that has the pad on the other side. To accommodate this, it is usually easier to use paper towel as a substrate initially. Since its thin, it will allow you to set the pad to only a couple degrees hotter than what the snake will actually feel.

If you are using some kind of shredded substrate you can set the heat pad to the limit of acceptable temps, that won't burn the bp, but will still heat up the substrate to the appropriate temps. Its important not to use too much substrate with this method, as the deeper you go, the hotter the pad needs to get. I find that if I am using an inch or so of shredded aspen for example, I can set the dimmer so that pad itself is around 93-95 or so degrees. With substrate on top, the temperature that the bp will experience is usually around 88. If the snake pushes all the substrate aside, 93-95 degrees is not going to be harmful. It might take a few tries, but you will find the happy medium.

Also, Im a big fan of the humid hide i previously mentioned. It provides a secure spot for the snake to soak up high humidity at their own choosing. It also serves as a humid sink that pumps out humidity into the tank continuously. I have found that if you just put wet sphagnum moss in the tank, the snake tends to spread it around and it just becomes part of the substrate. Also, if not allowed to dry out fully, sphagnum moss will mold. When you are using a humid hide, it creates a separate unit, almost a 'cage within a cage' system that you can pull in and out as necessary to clean, without cleaning the whole viv.

Just remember there's a lot of messing around with this snake going on. It's kind of necessary since trying to fix problems from benign neglect. But keep in mind this snake is highly stressed. Consequently, he may have shedding and feeding issues until he is left alone in a completed cage set up with no handling for at least a week, food offered and hopefully taken, left alone for another minimum two or three days for food to digest, before trying to get him used to handling. Just be patient with him. His whole world has been turned upside down and even changes for the good can be stressful, too.

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In regards to your question about the humid hide, you can put it in the hot side. The thing is that during a shed cycle the snake will likely prefer to be on the cold side of the cage. Also, the hot side is going to evaporate a lot of the moisture in the humid hide much faster.