That's gonna happen at first. Sounds like your know what you're doing though so I'll not go into basics. I'm assuming you're doing a version of the wwc method? You're going to be behind every tank with sand for the first year, but obviously exponentially better than a sand bottom tank after that. As far as your bacterial issue, it will subside soon with what they are saying to do.
Here's my tank, I'm at about 3 months right now, and I used aquatop clear magic to clear up my beginning cloudiness from bacteria/diatoms. I ghost fed used fritz zymere, and did a 10% water change every week, after the first 2 weeks and throughout the process. I also ran low lights for 8hrs the first month and then threw fish in at week 6 with another fritz zyme treatment, and switched lights to my ai prime 16hd, which is now running.
Send more pics when you get it stocked!