Why not just go back in and re-enable the controller?
In answer to your question though, a mainboard designer will program a BIOS to restore a "default" set of settings that will come in to play if there is no battery/battery dies/etc... This set will *usually* get the board up and running no matter what...so you can at least have a shot at troubleshooting it for problems. (BIOS Defaults)
Next, there may be a "normal" or "optimal" set of settings available. These are somewhat better than the default, and what the mainboard designer considers to be *best* settings for the board in the majority of circumstances. (Setup Defaults)
A "turbo" set may also be available, which can push the mainboard to its limits.
Of course you can always go in manually and adjust things to your liking...depending on the exact components you have installed, and a knowledge of what you are doing.