Standard format for custom symbols in schematic drawings?

You draw symbol the way your circuit is best readable and understandable. Techniques used are:

• grouping pins into busses;
• having space between pins groups per their purpose, usage or their connect destination;
• making comprehensive labels on the pins and on the devices.

From my experience reading circuits drawn using packages is a nightmare. Packages belong to board layout, not to schematic diagrams.

You may also find drawing circuit diagrams using packages inconvenient. There's always a choice for new device: make quick shortcut and reuse existing package as symbol, or draw own symbol, which takes time and real knowledge of device operation and pin purpose. I used to take time and draw new comprehensive symbol, and split large devices into logical blocks (symbols) for readability.

Both methods are used, therefore both are "standard".

Which one you should use is a matter of opinion, and a decision about which one better conveys the necessary information to the person reading the schematic.

For the person trying to understand the logical operation of the circuit, grouping the pins by function is usually better.

For the person using the schematic to figure out where to probe the circuit when debugging it, arranging the pins by their physical location is usually better.

As the guy drawing the schematic, you simply can't please everybody.