Here you can find info in spanish regarding CE and EE versions operated on Spanish Air Force.
http://fdra-aereo.blogspot.com.es/2013/04/cazabombarderos-los-mirage-f1-espanoles.html
On EE basically, a radar upgrade, new INS, refueling probe, capabilities to use the barax (ECM) on all EE fleet, whilst only some CE could do it, and the Syrel pod (ELINT). Also the EE could carry a bit less fuel due the space used for the new INS.
But take in count the Mirage F1 on Spanish Air Force, has been receiving small upgrades multiples times, until arrive to the deep modernization phase, resulting the Mirage F1M.