Hey horseno, I know this is going to sound odd, but for my tanks I don't vac my substate. If your tank is planted enough, the plants will basically eat up any waste that settles to the bottom. I just keep a good mix of cleaner fish, shrimp, corries ottos and SAE etc and let the fish help feed the plants and the plants help clean the water and supply 02 for the fish. I do a weekly
water change of about 5 to 20% of the tanks water depending on the tank. Add ferts and leave things be as much as possible.
And as far as mixing gravels etc, joy is right, the sand will eventually drop down through the gravel, but if you play with amounts, ie add some more as it settles you will eventually be able to get the natural mix your looking for. I have mixed substrate in all my tanks to provide natural zones for all my different fish.
About the only time I vacuum my substrate is right after a massive change in planting, ie adding or moving stuff around in my tank. As you upset the mulm etc and risk a
ammonia spike which will normally lead to a algae spike. And once your plants are rooted down nicely there is next to no risk that a vac will tear them out, you really have to give em a good pull to remove a healthy rooted plant (which i try not to do, if I have to move a plant, i try to dig away the soil as to disrupt the roots as minimal as possible as many plants like crypts will melt if you disrupt them). And for vacuuming sand, just down push the vac to the sand, hold it about a inch or so above and it will typically pic up the waste and not the sand.