I'm glad to read that. Too many people do exactly what I said and one day lose everything. But don't rely on the discs you've burned. Discs have been known to go bad over time and become unreadable. And I have personal experience here. If you want to burn them, make two copies and use two different brands. It's a good idea to have them on two physically different hard drives (not the same hard drive partitioned in to two sections). Finally, keep copies outside your residence - i.e garage, shed, family member etc, in case of fire or theft.
Back to your original question. There's no perfect method and you're going to have to find a way that you can live with. It evolves over time. In my case, I have a dedicated photos drive. Folders for all the places etc that I have photographed. I have a holidays folder and within, folders with all the places sorted by year. In each individual holiday folder are sub-folders by date, for each day. All the individual photos are renamed by date in the order, for example 2008 10 27 xxx where the 10 is the month and the 27 is the day, and xxx is each individual picture starting 001. This keeps all the pictures in the correct order. All my renaming is done very easily with ACDSee. If I edit a picture I will add an 02, 03 etc on the end of saved later versions.
The renaming strategy became important to me when my collection started running in to the tens of thousands, my camera had been round the clock, and I started producing pictures with the same file names as existing ones. It also makes it so much easier finding the folder where a particular picture belongs. Renaming is the first thing I do after transferring them off the card and deleting the obviously crap ones in a quick cull.
Like many people, I used to keep same-picture versions in different folders. A folder for raws, a folder for jpgs, and a folder for edited versions. It became too messy, especially when deleting a crap jpg and then finding the equivalent raw to delete. With them all in the same folder I can delete both side by side together.
As for downsizing for upload here, I have a folder named TP Upload which I copy the photo in to, and resize it (ACDSee again) in to another folder. I can't see any need to keep anything in the TP Upload folder after it has been uploaded. The original exists elsewhere, and the resized version can be remade in a minute if required. Nevertheless, as I'm not short of hard drive space, they remain for no good reason.
If you haven't got one yet, get yourself a good photo manager like ACDSee, for quick and simple viewing, organising, management of folders, photos, renaming, resizing etc. There are other programs that will be suggested, usually because they're free, and I've tried them all. ACDSee isn't perfect and I've had my ups and downs with it over the years, but it's the best one I've ever found.