In too many cases it is like the cashier who relies on the register to compute the required change, without it they are lost. Although apps can help at times there is no substitute for the basics and lots of experience.
One example would be designing a set of stairs. With one of the apps you don't know if it will work until you build it (expensive). Designing it by hand with a good sketch would greatly increase the confidence level.
As windows asked, what specifically are you looking for?
One is not to depend on your memory. Develop a checklist that is relative to your work. Make it/add to it details and don't get into a habit of ignoring what you think is not on this job. Go over every detail. Keep a notebook with you and if a thought comes up during work, write it down.
Organizing the tools: this can go out of control. Best way I found is those round bucket trays. Deep ones can keep wrenches in control but I wouldn't separate needle nose from chanellocks, eg.
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