I am doing something similar in my own app, using both pugixml and cocos2d-x. So I can confirm this combination works well.
Rather, because on iOS you cannot both read and write the data from and to the app bundle (which is read only), you will need to implement a simple check in the writable document directory - If you a saved file there, load it, if not, load from the app bundle.
So in essence for loading, if your saved filename is "my_save.xml", here is an example flow:
1) Construct a path for your save file in the writable folder by concatenating the writable folder path + your filename. CCFileUtils should have something like getWritablePath() for that.
2) if the file exists in the folder, load it. Otherwise, go to 3).
3) Construct a path to your original data file from the app bundle, using CCFileUtils::sharedFileUtils()->fullPathForFilename(). Load the file from there.
For saving, simply do step 1 and save the file there.