Georgee, hey! It's good to know you are still about and working on that application.
What I did was to organize the forms as per the document checklist, first the sponsor's, then the applicant's documents, then I arranged the relationship evidence. I arranged it according to type, separated by labeled tabs. So I had a section for
-emails,
-Yahoo chat logs
-Skype calls,
-MSN chat logs,
-letters of support from family and friends,
-our wedding items (invitation, receipts for services from the minister and the restaurant and copies of cards received),
-FB posts and
-financial support/matters (western union receipts, utility bills, grocery bills, credit card statements).
I also arranged our photographs on chronological (date) order, starting from some webcam pics first taken for each other to our wedding pics, honeymoon pics and outings.
It's really up to you how you want to do it. As each relationship is unique, so is each application. What you want to do is to ensure that everything is neatly organized and easily recognised by the IO.