Based on https://github.com/sebkopf/NSF-LaTeX-Template and https://github.com/mkmcc/nsf-template with code borrowed directly from these repositories and simply adapted for use with Lyx.
The usual disclaimer: absolutely no guarantee for accuracy or NSF compliance - you have to make sure everything is compliant with current NSF guidelines and the specific program solicitation.
Open, edit and render individual lyx files for each section. Instructions copied from the 2016 PPAG available in individual files but may be out of date. Render the 0_proposal.lyx file for a combined overview of the full proposal. However, fastlane requires individual sections. Code for splitting the PDF automatically is in the works.