in wooden vivs the best way to heat them is with a heat mat inside the viv, you can then put a piece of lino or similar over the top of it, iv got several sheets of newspaper on top of mine in the royals vivs but i will be getting some lino in at some point
2.0 Normal Royal Pythons - Q and Little One 1.0 Chihauhaun Mountain Kingsnake - Simba
Yes lyno is best if inside. If the mat is under the glass as you said I would put the probes on the bottom of the viv i.e. on the glass.
I'd do this because i'd have little to no substrate inside the "hot spot hide". I prefer this as it'll be 27-30*C there. If they want to cool down they can go to the cool end hide. Whereas if you have substrate in there and heat the viv @ substrate level to 30*C, as already mentioned the temperature underneath will be many *C higher- where your corn snake will burrow at some point.
Basically save the substrate for the rest of the viv where she/he can burrow and you know it'll never be too hot. And if she/he needs warming up, they have an accurate warm spot hide of 27-30*C.
Tbh I don't think there is any need to put anything on top of a correctly statted heatmat, absolutely no harm can come to your snake by only have substrate over a mat. If you are worried about your snake getting underneath the mat then by all means weigh it down, but not much will stop a determined corn!
Though none of my snakes have EVER been seen underneath their mats.
9.11 Cornsnakes 1.1 Hogg island boas 1.0 Dwarf Burmese python