We put our application in the exact order of the checklist titled -
Partner Visa: Offshore Temporary and Permanent
(Subclasses 309 and 100)
Application Document Checklist
We used no paper clips or staples as suggested and divided each section with pieces of A4 paper folded in half with a Title and brief description of whats inside. i.e;
Credit card statement (highlighted and commented on relevant purchases)
We don't have a joint bank account but we did have transfers to one another via paypal so we printed off statements and we were living in Italy and My partner was using my account and we had evidence of her depositing money into it etc.
We had separate sections for Finance, Proof of co-habitation, Travel and Holidays etc all divided with A4 paper folded in half around each section and titled.
It ended up looking really tidy and easy to understand in our opinions but i guess we'll see how it all goes and if it makes a difference presenting it well.
I strongly suggest you follow the checklist though and present it in that order.
All the best!