I would use foil tape on the heat pad that way if you every need to remove it it will be much easier. The thermometer prob should be under the substrate....I would just use a lamp dimmer for the che.
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This may seem like a no-brainer and I'm not trying to be dense, but when you say that you use the tape so that the pad can be removed easier, does this mean that you don't remove the adhesive protective backing? Wouldn't that melt?