You would need to either modify a default Skype package, and change its package name to something else (such as com.skype.custom), or find a pre-modified Skype package that's already been changed. Then enter this package name into the SkypeX preferences as the 2nd package. If you go back through this thread, there should be a post that has a pre-modified package that can be used as a 2nd Skype app.
I already know it and tried to modify skype apk with apktool. I disassembled it, corrected xml and rebuilded back, but it won't install after my manipulations. So I ask for some detailed manual about how to do it right. Here I saw link to 3rd version of Skype and don't want it.