I've done 2 dirt tanks with great results (so far).
On my smaller Evolve 8 tank, I removed the chunks with a kitchen strainer to give me a fine dirt and capped it with sand (1" to 1" ratio) and have no issues.
On my latest 40B tank, I just dumped the bag of MGOPS in and left the big wood chips in. My reasoning is as it breaks down, it will slowly provide nutrients and CO2 to the plants in the long run. I have this capped with sand as well and I'm seeing good results after 2 weeks running.
Also, prior to capping I soaked the dirt by adding enough water to make a thick brownie-like batter and let it sit for an hour or so and poking it a little to let any trapped air out. I capped it by starting with the perimeter, giving me a good reference on how thick the cap is going to be. I then used a plate upside down to slowly fill the water.