Hello,
there
must be an option to select ES device in Quartus device selection, but I yet didn't see it. If I understand right, Altera has shipped the ES devices with eval kit, thus support should be able to tell you how to create the programming files. Fortunately, I have no need to program ES parts, but I guess, there is an option. At worst case, it could be that the option doesn't exist in all Quartus versions.
Regards,
Frank
P.S.: For Stratix II, where a similar problem is said to exist, Quartus device selection offers separate entries for ES-devices. This option is missing for MAX II.