if i did a system restore would that only reset the settings of system folders or also folders like my documents

A Restore operation only monitors and modifies certain components of your system such as the Registry, user profile data, drivers, and program files such as .exe and .dll files.
System Restore specifically does not alter the contents of the My Documents folder, nor does it touch user-created data files (files with extensions such as .doc, .htm, .xls, etc.).
Being that SR doesn't modify the contents of the My Documents Folder (including any of its subfolders), any files that you have doubts about as to whether or not SR will modify them can be stored under the My Documents folder for safekeeping.