Honestly I would drain it all out. It will take eons for that to settle/filter out. Is there any cap on the soil substrate? Drain it until there's barely any water left, then pat down the soil and put 1" of your gravel cap and then fill by placing a saucer on top of the gravel, and pouring water onto the saucer. You have to go REALLY slow, and it will seem like it's taking forever, but after about 25%-50% you can start pouring faster. I did mine by dragging in a garden hose and letting it trickle onto the saucer and letting it go until it filled.
FYI, the first dirted tank I did looked like that also. I redid it twice before I figured out how to get it full of water without crazy cloudiness.
Also did you make your dirt damp before you started filling? Obviously it's damp now, but you want it the consistency of mud when you arrange it at the bottom of the tank. Not soupy, not to dry. Otherwise the "soup" will leach up above your gravel cap and it will again end up way cloudy.