You should never edit the actual citation in the document but the meta-data of the reference in your library. For example.
You have a citation (Smit, 2012) and want to change it to (Smith, 2012). You open the reference in Paperpile and edit the author field there (see below). After that you can reformat teh citations with "Format citations" and the name will be correct.
If you want to add text to the citation you can use the prefix/postfix fields in the citation details (see below). These changes will persist even if you re-format.
Everything else you add to the citation will be lost.
Hope that helps.