How does Startup Manager block startup apps? I am using the market app Startup Manager on Android, but I am a little bit concerned in the way that it operates. Is it effectively runnning every time as a daemon and thusly keeping the apps from not starting or does it simply change the bootable flag in the apps, without running in the background?
Some research indicates that this is most likely done by revoking permissions to the apps you specify. Specifically, the app needs android.permission.RECEIVE_BOOT_COMPLETED in order to run at startup.

However, while this is the most likely situation, I can't speak for the exact functionality of Startup Manager.

Additionally, if you're concerned because the app's description isn't clear about how it works, you can alternatively use Autostarts, an open-source Android startup helper tool which controls which intents actually get sent to which apps.