I think i went overborad with my organisation when I first started researching but maybe thats a good thing. I keep both an electronic copy and a paper copy of everything and use the same filing system for both.
I have split my generations up into books, book1 is my mum and dad, book 2 is my grandparents on my mums side, book 3 and 4 is my grandparents parents and so on (I'm only doing my mums side and my aunt has already done my dads ancestry).
Each book contains a cover page for each person wirth there own unique reference number giving there basic BMD details, a photo, parents names etc i also keep notes there on what i still need to research. I then have a second sheet for them which is a timeline of there lives, listing occupations, residences etc. Each of the entries on the timeline has a reference number for the document that holds the information which corrisponds to one of 3 folders I have holding my BMD certificates / Census returns / Parish records and other documents.
I find that whover I look at I can instantly see what book and sheet i should look at to see there parents, and where to find there certificates. All this is stored in another 2 ring binders at the moment, I can get about 5 books per ring binder.
All the same info i kept electronically as well, when i get a certificate or any paper document I scan it and name it with the same ref number thats on the paper copy, that way i can swap between looking at the paper trail and the documents on my laptop at any time. it also makes it so easy to update.
As for using Ancestry, i have 2 tree's the first is massive and goes back through alot of generations, i have to admit it's not all 100% proven yet but I'll get there. the second tree is private and only gets added to when I have definate proof of something.
I think maybe I'm really obsessed with the organising side of things
but when it comes to family research I think good organisation is key.
Good Luck with your own organising
Michelle