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Your question asked about available models. There are several but one of the most widely-used is EPANet.  It is a public domain program available free for download including good documentation in user manuals, and it is the basis of many other commercial models but with better documentation than most.  You can enter the elements such as the well, pump(s), tank and any number of valves with control features (pressure reducing valves, check valves etc.),  and of course pipes and their properties, PRV's may be especially important between zones if very different elevations.

If your elevated tank has an overflow, be sure to include an "emitter" element based on orifice properties, unless you want the model to assume there is an altitude valve that shuts off inflow when the tank reaches a designated level (instead of spilling out the overflow).