Thanks for joining the Community, @jprichardson86-o.
At this time, there's no way to include a reference number on expenses automatically. This would need to be added each time manually. I know how important automation can be for a business, and if you'd like to submit feedback about this you can do so by clicking the Gear icon on the top right, then selecting Feedback.
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On the other hand, this feature is available on sales forms where you can activate and set your own preference to use the Custom transaction numbers.
Let me know in the comment if you have more questions. I'll make sure to answer them. Have a great day ahead.