Well, we had three main sections:
1. Sponsor's forms and required documents (proof of citizenship/residence, Option C, etc)
2. Applicant's forms and required documents (ID, marriage certificate, etc)
3. Set of appendices ordered separately but grouped together. i.e. App 1-Photos App-2, Chat records, App-3 Boarding passes and entry/exit stamps (basically proof of travels and visits) and so on and so forth.
I arranged the photos in a document and captioned and numbered them. I did the same for the boarding passes and the entry/exit stamps: I scanned those and inserted them as pictures in a document, numbered and captioned them. This was, if we are referring to visits or anything in our relationship essay that needs some supporting document, we would say: please refer to App X, page blah, picture number B. Same way we can refer them to certain email conversations or dates that we want the visa officer to read.
It's very important to follow the checklist order for forms and those documents that they want as ID (passport copies, National IDs, Option C, etc) I wouldn't order it any other way than what the checklist suggests. But for the photos, etc I think it's more accessible to have everything grouped at the very end. My husband and I both wrote "essays" for our forms (the part that asks you to attach a sheet and explain if there is anything that can help them realize the relationship is genuine and continuing.) and we would need to refer to the same trip, same events, etc. Therefore, we decided to group is such, to make it less confusing. Otherwise we had to refer to "see main applicant package etc".
This way we could also order our photos and travel history chronologically. So if someone starts at the first page of our photo appendix, for example, and go forward, it will give them a visual representation of our relationship developing.
One more thing: since I wan't sure if they want to see the original boarding passes, I just put all of them in an envelope and enclosed it at the very end, but to be honest, I don't think it was necessary. I just decided to do so to be on the safe side.
Hope this helps to give you some ideas

BCG