Justin,
When you plan, you are planning the operation, not the gathering of paperwork to satisfy the regulator. There is no disconnect between the two in reality.
You're right, many are confused about how to operate legitimately, but I cannot stress enough how much easier life is when you step away from seeing achieving regulatory compliance as a separate task from operating.
If you operate well, compliance is child's play.
Others fly for operators who cannot work out where their passengers want to go, or spell 'available', or 'means', but that's another story...