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It is very hard to define guidelines for "system architecture", which is what you are talking about. Practice makes perfect. Yet, there are two tools you should definitely try using which will help you with modularization and standardization.
Use microchips as much as possible! This handy thing helps you organise everything and create modules.
On top of that you should use nodes. It can be used for naming inputs and outputs, for your own memory aids, or for anyone who might work with your creations.
On top of that, take your time with naming modules (microchips). A good name is one that is short but effective.
Hope this helps a bit.