Emacs allows you to select an e-mail program as the default program it uses when
you press C-x m (compose-mail), call report-emacs-bug and so
on; see (emacs)Mail Methods.
If you want to use mu4e for this, you can do so by adding the following
to your configuration:
(setq mail-user-agent 'mu4e-user-agent)
Similarly, to specify mu4e as your preferred method for reading
mail, customize the variable read-mail-command.
(set-variable 'read-mail-command 'mu4e)