You can set the encoding for a file by adding a suitable string at the beginning:
% !TEX encoding = MacOSRoman
% !TEX encoding = IsoLatin9
% !TEX encoding = UTF-8 Unicode
If TeXShop sees one of these lines, it will not use the default encoding set in the preferences for the file, but the one specified. You need not remember them: go to the menu Macros>Encoding and choose the encoding you want in the window that appears.
They correspond, in the same order, to
and the corresponding declaration must be issued in the LaTeX main document.
I recommend having the introductory string in the older files and then changing the default encoding to UTF-8.