It sounds like your doing exactly what your suppose to.
Mine is basically the same. My Tstat under UTH and use Aluminum tape to fasten...
Thermometer probe under thin substrate on Hotside (I use silicone to hold probe and wire) and the Head unit placed on cool side to read ambient & Humidity.
My Tstat is set to 98 on my UTH, thermometer probe reads 92/93 & when checking with Laser ontop of my paper substrate its 89/90...
Also keep in mind each thermistat can be 1-3 degrees off.. So keep substate paper thin in hot spot so you get the best idea of what your snakes basking temp is...
As far as ambient, i keep my thermometer head unit about 3" off the floor of the enclosure cool side so it reads ambiemt down low where snakes spend their time.
My thermometers have all 3 displayed.. Probe=Hot side/Head unit=cool side & Humidity.