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When I had FiOS installed I got a flyer on my front door saying a subcontractor would be laying the fiber from the telephone pole to the house and to call them if you have an irrigation system etc. I did, told them I had one and how I was going to mark the system (putting flags at the heads and near the well head). No issues with the installation.
For your own piece of mind, look for irrigation system not keeping pressure or excessive pump recycling in addition to testing your system after FiOS is laid.
All that is well and good, but if the contractors are bozos, there's nothing that can help you. Verizon came early and painted all over our lawn where every utitlity and exisitng cable line was buried. Additionally, I indicated with clearly-labelled flags where we had an invisible pet fence wire running through our yard. Regardless, when the day came, these minimum-wage apes sliced through both our invisible fence and the cable line like they were butter and didn't even bother acknowledging that they had done so.
You can only do so much.