You guys might want to consider apktool also ([UTIL][14.06.10] Apktool v1.3.1 - a tool for reengineering apk files - xda-developers)
It decompiles all of the xml's and the resources. It also handles the baksmali for the java classes. There is a bit of an issue on the recompile side but I generally just take the recompiled files I need and put them in my original apk.
The nice thing about it is that it decompiles your 9patch images so you have the original stretch lines.
Apk Manager has apktool.jar in it. That is what it uses to decompile and recompile the .apk. Only thing is you don't have to type out the commands. It is a simple type 9 then 11. Also Apk Manager has the signing and zipalign tools inter-graded.