I would start by chosing what software you will use to design the PCB, have a play and read some tutorials.
Then read the datasheet for the 32u4 - is it suitable for your needs? You might be better using the chip from the Teensy 2.0++ instead as it has more pins and more memory for firmware while being basically the same. Or not (maybe it uses more power? Do you need lots of pins with bluetooth or are you going for portable and not backlit? If you have less pins and thus less switches you need more layers...)
USB is the same whatever connector you use so that's first to add (there's a schematic in the datasheet) Start with a big PCB area so you can see everything clearly.
Then you need to find/design schematics for battery charging and bluetooth and add them.
Next cram everything into the smallest space possible - this is the hardest part.
Then lay out pads for all the IO pins and attach them to the controller chip - more trace routing fun.
Finally get a test sample made. This will be expensive - there are usually price breaks at 10/25/50 units but who wants them if they don't work. If you can hand solder everything that will keep the cost down but it's going to be small and cramped....
Easy to write out, not so easy to do
