You'll need to set some environment variables for both the external libraries, and ScummVM itself. This is so the right compiler and libraries will be used.
export SDKROOT=<your toolkit directory>
The below should usually do the trick for these:
./configure --host=arm-darwin --prefix=$SDKROOT/sys/
make && make install
=== ScummVM ===
Then, we need to configure ScummVM itself.
./configure --host=iphone \
--disable-mt32emu --disable-scalers --enable-release \
Note that the --with-flac-prefix (and the rest) is only necessary if you want to include support for that specific library.
Now, we can start the compile:
Lastly, we want to make a ScummVM.app bundle:
Then simply upload the whole ScummVM.app directory to your device under the /Applications folder, and you're done!