CAD Schematic pin arrangement approach
This is a no-brainer, use the functional layout approach.  There are a lot of bad schematics out there, including professional ones, so you will see pin order schematic layout sometimes.  However, it is a bad idea.

Pin-order symbols is mostly laziness on the part of someone defining the part in the CAD system.  Slapping everything down in the pin order is easier than digging out the full names and functions of each pin.  Of course this isn't usually the stated reason.  The most common excuse is that it aids in debugging.  However, a little thought reveals that is not so.

When you are debugging a new board, you have both the board and schematic in front of you.  Think about the usual work flow.  Which is more common: "I want to look at the clock line, which pin is that?", or "I want to look at pin 5, which function is that?"?.  Clearly the answer is the former, by a lot.  Yes, occasionally early in the debugging process you may want to go around a IC and look at the signal on every pin, but that is usually once, if at all.  There are cases where pin-order helps, like for some repair work, but for every one of those there are multiple cases when function order is better.  Functional pin depiction is actually better for debugging than pin-order depiction.  Don't get taken in by the excuses for not spending time on the symbol definition once.

Then there is the other considerable issue of schematic clarity.  Here there is no contest at all.  Pin order obfuscates the circuit and either forces a lot of air wires or forces other blocks to be put in inconvenient places.

For more on good schematic practises, see my more lengthy writeup on the subject.