Set the kill level to safe, frequency to on screen close and security level to med or high.
Let the phone boot and after a couple minutes open APK and ignore the apps you want running. The phone should take care of itself past that. To save battery I do not ignore twitroyd and imeasy..those are program I want to manually kill since they are battery drainers when running for more control over my battery.
I use Handcent instead of messages and even though the messages app is not set to receive it still shows up after killing it. My friend said that is how Android/Linux is..just because an app shows running in the background does not mean it is using any battery, although some do..not all do