Mr Tuffy liners can wear a hole in your tube and cause a flat. The problem is getting everything to lie down straight and flat in a small space, without disturbing it by mounting a tire. Liners can be very useful riding around goathead thorns, otherwise leave liners alone.
The best way to generally minimize flats is use a tire designed to minimize flats. These tires have more rubber in the tread, plus supposedly puncture resistant (
PR) additive layers. I don't put much stock in these claims. Some of the
PR material is simply scrap kevlar material, ground up and added to the rubber compound before molding/curing.
The best way to generally maximize punctures is to ride a very narrow, lightweight tire. Not much material in the tire to stop intrusions/punctures.
I've had remarkably good luck using plain ole tires and tubes and velox tape. I always inspect new rims for sharp spots and file/sand/bang em down smooth. Drag a cotton ball lightly through a rim channel before you add tape - the fibers tend to hang on sharp points, makes them easier to locate. Finally, the most important point - pick a clean line as much as possible, avoid riding through road debris. Avoid the gutter area at all costs.