I haven't gone back and read through this thread to see what inhabitants you have in your tank, but if shrimp and MTS are part of the equation then I'd go with the 1-2mm size gravel. Much easier for the MTS to burrow in and the shrimp will have an easier time picking up smaller pieces of gravel as they go about their shrimp business. As JohnWesley has pointed out, rooted plants will help prevent anerobic soil conditions, as will MTS. I'm pretty sure Diana refers many times to the role plant roots play in oxygenating the soil. Regarding the depth of the cap, whatever size gravel you decide on, 1 inch is the maximum recommended. You could use less if you want...its main role is to keep the soil from getting into the water column.