They use SUBSILVER as a refrence, but basically if a mod calls for editing of a /templates/subsilver/[FILENAME].php, you should do this there as well as on any themes you install. (Just incase you want to go back to Subsilver). If you have EASYMOD, it will try to install the mods on all of the installed templates (it doesnt always work, since templates are varying). You dont need to remove the FLAGS mod, though you may need to manually do the mod to the new themes.
Hope this helps
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