Oh. yes you can do that.
For best results follow:
1. Create new folder inside my apktool folder.
2. Rename it to "com.google.android.googlequicksearchbox" [Or whatever app you want to theme.].
3. Go back and open android[Or any folder present there] folder and copy apktool.yml and AndroidManifext.xml .
4. Reopen your newly created folder and paste the two file you copied to this folder.
5. Open apktool.yml using notepad++[If you are a Windows PC user like me] and change "apkFileName: android.zip" to "apkFileName: yourfoldername.zip" and save.
Now when you will use apktool to recompile it you will get a .zip file instead of .apk file