I have been using Brightwell's BioFuel and Microbacter7 for several months now with good results, at least in terms of coral coloration. BioFuel is basically a diluted carbon source and is a little easier, in my opinion, to dose safely (as compared to vodka). I am currently dosing 11 drops of BF and 14 drops Microbacter7 each day. I'll probably start to move towards bi-weekly dosing. In a few weeks I'll also begin adding some amino acids. This system is analogous (and a lot cheaper) than using PolypLabs' Reef-Resh.
I've never had high nitrites and that's even after using dechlorinated tap water for top-offs and lately, for water changes too. Nonetheless, I do have some green/brown algae issues (I have to clean the glass daily, but that's about it since it doesn't grow significantly anywhere else). Anyway, my phosphates remain undetectable on the Salifert test kits (which, like all phosphate test kits, are pretty inaccurate).
My advice would be to use coral coloration and algae growth as a guide on how to adjust dosing. As mentioned already by others, stick with one system and stay consistent. You might want to keep a journal to help keep track of things.
Edit: Oh, and, I have also noticed that my skimmate is generally darker than before.