For arguments sake Pixey, let's say that you are programming a fun card, so you are in the fun/atmel section.
There will in most cases be two files, not three, although there is a facility for programming an internal Eeprom.
The Flash file could be called almost anything, but does quite often have flash in the file name. The Eeprom, normally has Eeprom in the file name, so you can use a process of elimination.
If it is similar to the Elvis, then you load both files and then press program and Voila.
PS. I would use the Dave M files to start off with as they are very clearly marked and well documented, if there is a choice of flash files, use the ones with the H (Humax) prefix and not the Fr (Freecam) ones