Is there a better way to utilize the flash memory than:
1. Disconnect the card.
2. Setting CFG_SET1 to ON-ON-OFF-OFF.
3. Connect the card.
4. Write to flash using openFPGALoader --board olimex_gatemateevb --write-flash blinky.bit
5. Disconnect the card.
6. Setting CFG_SET1 to OFF-OFF-OFF-OFF.
7. Connect the card and observe the stored configuration run.
Pretty much, yes.