Time to put a system in place, without a doubt.
I have a laptop and a desktop computer. I also write on the computer at school and the one at my part time job. I use a flash drive to carry the files from place to place (though, I then email a copy to myself because I've had two flash drives fail in a year!)
When I get ready to leave for the day, I put the most current file on the flash drive (for any and all stories currently in progress.) I go do my thing, working off the flash drive while away from home. This can be risky, but so is storing things on a harddrive. As soon as I get home, I plug the flash drive in and copy the changed files onto my desktop. Then I work off the desktop version.
I save almost nothing on my laptop. I just store it on the flash drive. The few things I do put on there, I move to my desktop via the flash drive or over my home network. See-- ALL my files go home to roost on the desktop.
In my email, I set up a filter so that if the words BACKUP appear in the subject line, it automatically goes into a backup folder I made. This way, it doesn't clutter the inbox. I always write the subject as "BACKUP: [Name of Story]. The email does a time and date stamp. Since it's all in it's own folder, I don't have to worry about wading back through inbox messages to find it. (And, with my email, I also have a copy in the Sent file since it automatically stores the sent emails.)
On my desktop computers, I have a folder for Writing. (My OS is on the C drive and my work is all on the W drive.) In the folder, I have sub folders seven or eight deep, sorted into all sorts of ways. Short Stories, Novels, In Progress, Ideas, Writing Advice, etc. In the Short Stories folder, I have folders for each story and all it's versions, notes, etc. Everything ends up here (and is backed up regularly from here as well. I make CD's three or four times a year of my entire HD. Well, DVDs, now.)
As for notebooks, I strongly recommend using one notebook for writing, one for school, and one for work. Or, another option, using scrap paper for quick jottings. Then, the important part, move those notes into more permanent storage.
I have a small hanging file folder holder on my desk. I have a folder for story ideas. I try not to use it much, and instead type the files up and put them into the appropriate computer folder.
I have a small notebook specifically for notes about my novels. I jot or copy ALL notes about my novels into that notebook. So if I'm at the store and all I have to write on is the back of a receipt, once I get home, I'll copy that tidbit into the appropriate place.
I'm not an unorganized person. I've got laziness running through me that I blame on a faulty gene (ie, my parents). But I have systems in place to make sure that I don't screw myself in the end.
Oh, I also have a box. Three, actually. I poached some banana boxes from the local grocery store and put them on a wire rack. Each is labeled-- Writing, Real Estate, Grad School. WHen I have things that I need to hang on to but that don't need a permanent storage solution, I toss them into the box. And it keeps things together for later sorting without being a horrid pile of random papers. It's a box of related papers. Not great, but it really works for keeping my office clean. I just need two more boxes... ;-)
Okay... long winded, but what it comes down to is:
You need a system for keeping organized
You need to be disciplined about using that system (or the system is worthless.)
Poach ideas that work for you. Develop a routine for how you get ready for your day/ work and how you end/ 'clean up' at the end of the day. And stick to it. =)
Best of luck. Losing things sucks.