Keep in mind that the dirt layer will compress over time as the organics are broken down. Sand is a much better cap than gravel since it seals the dirt layer, preventing any dirt from seeping up into the water column. The methane buildup is due to anaerobic conditions from using a too fine of a sand. Having plenty of heavy rooting plants will bring oxygen into the substrate preventing the anaerobic conditions that produce methane gas. Malaysian trumpet snails also help keep the substrate aerated. With dirt tanks, the gas that is produced in the substrate when you first start out is CO2. This can be beneficial for growing your plants. If it's too much of a problem, you can use a bamboo skewer to poke some holes into the substrate to release some built up CO2 but not all at once. As for replanting, some recommend against it but I will often trim and replant a few stems every other week. A little bit of dirt may pop up but I usually vacuum whatever ends up on top of the substrate. A pipette and some extra substrate helps for touch ups. Other than that, I'd go for at least 1.5 inches of dirt capped with at least an inch of sand.
RAOK Club #77|The Fraternity of Dirt #112