Default [Q] [Xperia J] How to change apk in rom stock?

Hello, Well I am new to modifying roms and I have a big doubt.
Now I'm using the stock rom JB .31 on my xperia J, however I want to change what is the notification area to put clear, but I'm not sure modify the framework-res.apk or the systemui.apk, fearing rom being that stock, this has a brick.
I would also like to modify other apps to set background transparent, like Gmail, Youtube, etc. ..
If someone could advise me on this, I would greatly appreciate.