Dirty,

The question is what is your system needs and is either of them giving you what you want for the cost. We need more info than what you provided. Give the breakdown of the heads per zone, the make an model of the heads, pump flow(gpm or gph) and pressure(psi) at the ground surface. Both their answers may not reflect the most economical way to irrigate with your pump($$). The guy who says your system's zoning depends on your pump's flow and pressure is at least trying to plan and communicate with you how he came up with a design. The other bidder is trying to keep you in the dark but he knows from looking at your pump and testing it, without you knowing it, what the pump can do and you shouldn't worry your little head about the mathematical complexities of the situation(warranty?)(BBB history of the bidders)(who has a Contractor's license and insurance). Let us know the two itemized cost of the bids and we can help you analyze them.
I would get a third bid and that will increase you knowledge of the local costs for this type of work greatly. Don't let any of the bidders rush you into a decision. JMHO and Aloha