The Administrator account is just another user account but with additional privileges to modify HKLM branch of Registry. As Ivo said, if you want one set of settings and menu items for admin account and another for all other users, in HKLM, add the settings which will be common to admin+other users (since HKLM applies to all accounts, including admin account on that PC). For the admin account, in HKCU, add the extra settings/menu items. For menu items, the registry value is "MenuItems1" or "MenuItems2" or MenuItems7" (depending on which style of the menu you use). To prevent the menu items from getting locked down via the Settings UI, only add them to HKCU via the admin account.
Under HKLM when you add any registry values, they will be locked down, that is, only admins who have HKLM registry access can change them. If the settings you add have _Default appended to the value name e.g. EnableContextMenu_Default instead of EnableContextMenu, they won't be locked down. Instead, only the defaults will be changed.