vacuuming the substate is the best method I know. I also started using a PURA filtration pad in my sump 2 weeks ago and everything perked up in the tank.
Not sure how it would impacy nitrates. Claims to remove: Solids, Organics, Ammonia, Phosphate, Medications, Lead, Copper and silicates. Others have spoke highly of them as well. You could also add some nitrate sponge in a nylon bag.
One thing to watch is the amount of bioload you are adding at a time. I know you have been doing a lot of stocking lately. You may need to hold back for a while and let your filtration catch up.