Cyclone II - configuration

If you are referring to user mode where the dev board boots from a user specified program instead of the out of box demo program, you must make a physical change on your board. For the EP2C70 board, there is a jumper on J29 that you must move. In safe mode it is on the top two pins, and for user mode, you must remove it and replace it on the bottom two pins. The board can now be programmed and will run in user mode. If that is not what you are referring to, please be more specific with your question. Hope it helps.