QMK configurator is great, but requires your keyboard to be in the grand list.  For 100% custom designs, you have to put a bit of effort into it.  This is the workflow I use. 

Step 1: Develop the layout here:

http://www.keyboard-layout-editor.com/

Key labels are handy but not necessary. 

If you need a keyboard plate, you can pop the output into this handy site:

http://builder.swillkb.com/

and you get a cad file suitable for laser cutting or, with a bit of effort, 3d printing. 

Next, hop on over to here:

https://kbfirmware.com/

and use it to assign actual key functions to the layers.  Unfortunately this bit of software is very out of date, a bunch of keys are missing and most of the fancy keys such as LC don't work when you try and import them.  It's still quicker and easier to get a rough layout than to do everything by hand. 

Once you have the keyboard layout go to settings, then save configuration.  This will give you a JSON file that you can import into the QMK command line suite  with

# qmk import-kbfirmware <name of json file>
you can then go into the keyboards/<keyboard name>/layout folder and edit the default.json to fix or add whatever features are needed