I use .060 Kydex in my sheaths. I cover the blade w/1 layer of tape on each side and I space the blade out w/ a thin piece of leather before molding.
When molding, I heat the kydex to around 325deg.F until it is rubbery and quickly mold it to the knife. I mold my sheaths tightly at first, then loosen the handle area w/ a heat gun until it fits properly. The leather leaves just enough space in the sheath to avoid the worst scratches, but not so much that the blade flops around in the case.
The biggest cause of scratching is debris left in the sheath during the sheathmaking process. A grain of sand, metal dust, or sandpaper grit can become molded into the kydex, causing a lot of headache. The thing that helped me a lot was to clean the sheathmaking area very well before beginning, and to keep the tape on the blade until the sheath is fitted.
After the sheath is finished, I blow it out w/ compressed air, swab it out with a piece of clean rag on the end of a clotheshanger wire, and blow it out again.This usually removes any debris hung up inside.
Also, I drill a drain hole into my Kydex sheaths near the knife tip area- this makes it a lot easier to clean the sheath out for you and the user.
One final note- I have found flat-backed sheaths tend to scratch more if you mold the sheath w/ the knife sitting at an angle( blade and handle both touching the table/surface)- I have had very good results molding this style sheath with the blade laying flat on the table/surface, and molding the handle area equally on both sides of the sheath. Hope this helps- I fought with the same problem at first until I experimented a little.