Matt,
Yes Bio S is for the intial cycle, you can go longer if you want, but not necessary. If you are wanting to use the Probiotic aspects of AF, then yes, the bacteria and carbon source are necessary for this application(Pro Bio S, NP Pro). If running AF Reef Salt, it is not probiotic, so you do not have to use NP Pro and Pro Bio S, they are just tools to help you run your tank very low in nutrients, but if you have another method, it is possible to use some of the AF supplements, minerals, and trace without running the system ULNS. Some utilize a big skimmer and based on the bio-load do not even need to run the Probiotics, but others such as myself do, mainly because of a heavy bio-load. Hope that helps man! Cheers!