Currently I use permissionsex and jCommands. I want to switch to essentials because it has a chat system that factions uses. Will I have to remove permissionsex and jCommands to install essentials?
no, but you will have to add the permissions nodes for essentials and remove jcommands. essentials is designed so commands used by other plugins override the essentials ones.
It depends if the commands are totally the same. If it is then the server wont know which plugin to associate it with, thus ignoring it.