I wouldn't use a substrate, to easy for them to get impacted i think, but everyone has their favorites and reasons why they're the best of the best. to each their own
I used a mat for the first year, give or take, i had my gecko (i've had him 2 years and a few days now so i'm far from an 'expert'). I'd spot clean it until it got dirty, then i'd take it out and hand wash and rinse his bathroom area. After a couple wash/rinses the mats will shrink, then you buy a new one.
Rather than spending 15 or so bucks on another mat, i switched to paper towels, I use the "free of everything" type towels. he seems to be more active on the towels than he was on the mat. 2 layers of paper towels vs the mat didn't need any recalibrations on the thermostat to keep the warm side up to temp either. Lots better on my pet budget also 6 rolls for about 2/3 of what a mat costs, takes 6 or 7 sheets (trimmed) to make a double layer.