As a very rough guide, this was what I did to get the sim working directly from the build directory:
mkdir build && cd build
./tools/configure --target=ipod6g --type=n
make
make full-zip
mkdir simdisk && cd simdisk
unzip ../rockbox-full.zip
cd -
./tools/configure --target=ipod6g --type=s
make
cp ../uisimulator/bitmaps/UI-ipod6g.bmp UI256.bmp
rm -f simdisk/.rockbox/codecs/*.codec
cp ./lib/rbcodec/codecs/*.codec simdisk/.rockbox/codecs/
./rockboxui