If you're confused by all the stuff, you do not need to mess with any of it. Just move the slider at the top to the desired speed. It will still down the speed when it's not needed. The profiles are just for when you don't want it to ever at max speed. Like if you have a 1GHz kernel installed you can set a profile for it to never go above 600mHz while in sleep mode. The rest of it you don't need to touch.
It might have got the unistall fail because it was installed to the sd, BB has a setting that tries to install all apps to SD which causes problems with some apps. You could check your settings>applications>installed on SD to see if it's there.
I don't know about the minimum setting. If you uninstalled it set there, it might have kept it at minimum. But BB has script to manage overclocking, so SetCPU isn't necessary I don't know if it would override those setting. Did you try and reboot and see if it's still laggy?