What U'll Need: 

-Java Jdk installed in your PC- Here
-ApkTool - Here
-SignApk- Here
-framework-res.apk - from your phone
-Mediatek-res.apk - from your phone
-org.cyanogemod.platform-res.apk (if you are to use cm apps)
-and the Apk you want to decompile,say SystemUI.

Now with the main part XD
-Setting up apktool
-Make a folder in any drive and keep Apktool and the apk files mentioned above.



-Hit ctrl+shift+Right click and click on 'Open command window here'
-A command window will open just like this
-Type "apktool if framework-res.apk" hit enter and "apktool if mediatek-res.apk" hit enter
 (this will install them as base framework)

-Now type "apktool d 'appname.apk' (Ex:apktool d systemui.apk)
 (this will decompile the app and create a folder)
-you will get to see this :)


-Open the folder of decompiled apk and edit as you like
 (don't do anything you are not sure about)

-Now in the command window type "apktool b outputfoldername" Ex:apktool b SystemUI

-Go to /dist folder and take your newly built Apk :)


Signing the Apk:

-To sign an apk download the sign-apk.zip
-extract it to any place.
-move the newly built apk into this folder
-Hit ctrl+shift+Right click and open command window

-Type the following
  java -jar signapk.jar certificate.pem key.pk8 path-of-the-folder-contaning-the-apk \apk path-of-the-new-   signed-apk \apk
 EX:
  

And Done ;)



Video Tutorial: