So typically there's a couple of things that need to be met to build in a flood zone, but first and foremost, you NEED to contact the local jurisdiction to see if the exact location can be built on and you need to confirm their conclusions based on looking at their ordinances (city if it is incorporated or county if it is unincorporated, in most cases; some places the state-level). Don't trust their yay or nay 100% in any case.
First key to building in a flood plain (and getting a building permit in a floodplain) is freeboard. This is the minimum elevation above the Base Flood Elevation ("BFE") that the lowest occupied floor must be. Typically this is 1'-5' above the BFE listed in the FEMA Flood Hazard Map, depending on the local code.
If the building is designed to meet freeboard requirements, the next requirement is typically that the building be engineered to adequately withstand the anticipated loads placed on the structure during a flood event. So yes, typically you will need all plans signed off on by a P.E.
The third common component is a study showing that the additional fill placed in the flood zone by your planned building will not significantly decrease the water holding volume of the floodplain (in addition with other permitted or built fills in the same basin). There is usually a cap on the amount of fill a particular basin. This is more impactful in floodways (vs floodplains) and with built-up foundations (vs. stilts/piers which have less volume).
You will also need to consider potable water and wastewater issues. Many areas do not allow water wells in floodplains or require certain design features in them, the reason being that they are very susceptible to intake of floodwaters which often cause contamination. Sewer is often not available in floodplain areas and many areas do not allow septic to be installed in floodplains, or require specific design features.
Sounds like you may have a good bit of due diligence that hasn't been done yet to really be able to make a decision on if you can even develop this property. I'd suggest hiring a professional or really digging into this yourself.
My background: over 8 years in environmental consulting (13-present), 6-7 yrs doing floodplain development permitting across the country for telecommunications, commercial real estate, and oil & gas.