Decide where the filing system will be created, depending mainly on: sensitivity of information, budget, IT savvy, system maintenance etc. Options available are Dropbox, Google Drive, shared folders or setting up a file server. You can also take advantage of technology resources specifically for non-profits, such as www.techsoup.org, www.grassroots.org, or www.npower.org.
Set up the system. All available documents are properly labeled and filed into the new system.