It seems the easiest way to change or theme icons is to not unzip them. Just open them with 7zip and make your changes, then close it. They will stay compressed and all of the info and size will remain intact.
Once changed you will have to resign the apk or zip file.
I spent the better part of 2 hours reading up on it using these forums and google, but I do not in any way feel knowledgable enough to instruct you on the finer points. There are oodles of topics on editing apk's and signing them when you are finished.
The steps seem pretty clear:
1. download or pull apk
2. open with 7zip
3. make changes keeping sizes and file names the same
4. close
5. re-sign the apk or zip file (most likely have to delete the existing files to the original signing which will be replaced with your own)
6. push or install the zip or apk (make sure the original app is uninstalled prior to reinstalling the changed app)
There are various methods and tools. The most helpful thread I found on signing is here:
http://forum.xda-developers.com/showthread.php?t=473580
I hope this covers it all and is helpful to you. I am new at it and can only tell you to backup everything and if you are unclear on any of it, then don't attempt it.
Read all the posts related to it. There is great info and plenty of feedback on known issues or mistakes others have had.