Yep, that's how I do it. Except you dont have to rename your apk files, they'll open up in archive just like a zip. With jar files I just push without having to drag anything to the original and they'll work.
If you ever decide to modify the framework-res or certain system apps like secsettings, camera, contacts, and probably some others, I have to do those with Windows and winrar because they dont seem to work with the normal compression mode. Winrar lets you change the compression mode from normal to store. Thats the only I can get those working.
But for SystemUI and Settings the regular compression mode will work, correct?