One of the major reasons people will venture into making their and designing their own keyboard is that they want to use a special layout that isn't readily accessible as a premade keyboard. Designing a layout is as easy as moving keys around on a pre-existing layout (like moving the numpad onto the left side instead of the right or deleting extra keys) or changing the angles, splitting, and stagger of the keys to make it more ergonomic. 

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For this I use keyboard-layout-editor.com it's a really good tool to visualize and create layouts of your choosing. I will usually start with a preset board (accessed on the top left tab) and go from there. The tool is fairly intuitive, but here are some shortcuts that make it much easier navigate. At this point, don't worry about having the correct legends. The only think that is important at this stage is the size and position of the keys. (If you are not sure of the size of the key, select it and it will tell you the size under the Properties tab)

 

Identifying the size of a key - Select a key by clicking on it and it will tell you in the Properties tab under Width

Selecting a group of keys - Drag the mouse to the outside of the keys that you want to select. Once selected their outline will turn red

Re-positioning keys - Select the key(s) you want to move and use the arrow keys.

Resize selected keys - Shift and Arrow Keys

Add a new key - Insert

Del - Delete selected keys

Copying and Pasting keys - Ctrl C/V

Undo changes - Ctrl Z

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When considering non-standard layouts, be aware that it may be harder to find keycaps. Be especially weary of caps that are under 1u width, 2.5u, 3u-5.5u, or anything above 7u as those are nearly impossible to find. 

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Once you have finalized the layout of your choice. You will want to click the Raw Data tab and copy everything listed and put it in a safe place. (This will become important in the building and design of the plate and case.