Basically this will just make everything more convenient since it will allow your apps to run automatically once your phone boots up. So, there's no need to open them manually or worry if they are really installed or not.
*Please do not do this on games*
Some apps that can be changed are
5. home launcher
6. and many more...
What you need to do is to download the apk file then also download root explorer (look for it on apps page)
You need to use root explorer and go to system apps and set to r/w (read and write)
If you have a modded apk for camera "camera.apk"
To replace stock camera just move the camera.apk to system apps and replace the one that is on that folder and reboot phone!
You can also do this for home screen
If you have holo launcher and want to replace it to go launcher
Browse through system/apps then delete the home launcher apk and replace with the launcher you want!
** Always set permission to RW-R-R (see tweaks tab on how to set permissions)
This goes on too for music apk or any other apps you want to set as system app. Just place it on system/apps and set correct permissions even if app has nothing to replace..