android app install overwrites /data/data/com.my.app
DO NOT create the folders before the app itself does, as you often won't be able to get permissions, ownership and contexts right. Instead, after a new install, run the app once to let it create the file structure, then proceed to overwrite. It's also highly recommended to find which exact file(s) stores the preferences/data you want to restore - usually just some XML files in shared_prefs sub-folder - and restore them only.

The final solution to such problems in the future would be just using apps like Titanium Backup to automate the backup/restore process.

EDIT: I downloaded Zoiper myself and tested: I modified some preferences, backed up /data/data/com.zoiper.android.app/shared_prefs/com.zoiper.android.app_preferences.xml, then cleared data and re-ran the app to let it generate structure. I restored the pref file afterwards, and they did get restored after I did the 1st trick. The thing is, don't forget to first force close the app before you try to replace stuff, or the running app will simply ignore it.