If you're using Factions, you place the JAR file inside your plugins folder and start the server. By default, all land is Wilderness and to claim safezone (it claims the chunk in which you are standing) you say /f claim safezone -- you must either be op or have a permissions plugin with perms set-up correctly. Google 'factions permissions' and 'factions config' for permission nodes and for the configuration guide. Remember, when editing the config while the server is running, you must first /f lock on then edit the JSON files, then /f reload <name of edited file>, /f lock off, or edit it in-game via /f config -- otherwise it gets overwritten!
It sounds complicated, but it's not really.