I have recently been using a very neat software tool that I have found very helpful in assembling grant proposals and other academic writing: Scrivener.
Sorry, this is Mac oriented software.
Originally, this software was designed for fiction writing and script writing. However, it has a number of features that make it a very useful tool for assembling your thoughts, notes and references that can then be compiled automatically into a formatted paper or proposal.
As I was putting together an application for an IPH Catalyst Grant Proposal, I created a generic template for IPH Catalyst grant proposals that others may find helpful.