As an additional step you can add two lines in your .bashrc file from your $HOME folder:
user@host ~/.bashrc ... export PATH=$PATH:~/m68k-cross-tools/usr/local/cross-mint/bin export PATH=$PATH:~/m68k-cross-tools/usr/local/cross-mint/m68k-atari-mint/bin</pre>
In the end you will not have to retype all the export commands each time you launch Cygwin.
Note: '~' means current user $HOME folder.
Setting up SDL and other libraries
First thing is to get the sources of SDL. You can grab the sources from Patrice Mandin's webpage or get the latest snapshot from official https://github.com/libsdl-org/SDL and rebuild it from sources. Rebuilding from sources is recommended, because it guarantees the proper installation of libraries in your environment and there is possibility to generate debug symbols.
First thing is generation of configure script, after that we will be launching configure script, we will compile and install library afterwards. Very important is the --prefix switch. It must point to the directory, where cross compiler is installed. If it will be wrongly specified configure script will be unable to find falcon.h, mintbind.h headers and will be unable to find the correct tools.
./autogen.sh ./configure --disable-threads --enable-static --disable-shared --disable-video-opengl / --host=m68k-atari-mint --prefix=/path/to/usr/local/cross-mint/m68k-atari-mint make make install
If everything will be all right then SDL will be installed in /path/to/usr/local/cross-mint/m68k-atari-mint.
note: When I've downloaded SDL from repository I've had some errors related to bad file encoding. If something will go wrong while launching autogen.sh script then for sure there is something wrong with script file encoding, converting file to UN*X line endings will solve the problem.