I found it helpful to not change "complex" outputs directly, but rather call a function that does that for me and handles the complexity in one place. For instance, if a brake must be removed before activating a motor, rather than pasting the same code every time you need to use the motor, wrap that in a small function block and use that.

In general, make the code easy to interpret, especially when debugging - which means organizing your code and using simple abstractions. State machines can be useful because they're easy to interpret if you comment your states, leading to high-level understandings like "the machine is waiting for an item" rather than "it will do something when I0.5 goes high".