The patch tells it what file to apply to. The header should be something like (view it in Notepad or your fav text editor):
--- Folder/old_file
+++ Folder/new_file
In the case of a Subversion patch, you'd have revision numbers as well (since the file names are the same).
GNU patch will let you override those names, but I don't know of any GUI tools to do the same. I'd check with the various diff programs - though, it does not appear WinMerge supports applying patches.