I will like a recommendation on how to perform a 1,000 ha survey with FMX, multiple benchmarks, etc. and get good data for making the design.
You could do that but you should try and have them on the same master benchmark if possible so that all have the same horizontal and vertical data. And it's probably got already surveyed in multiple fields rather than one large field because the FMX can get bogged down with that much data. As long as each field that you survey have the same master benchmark, ideally in the center of the 1000ha field, then it will be on the same coordinate system which is a good start. Boundaries are not that critical, you can adjust those boundaries in OptiSurface Designer.