I've changed my file structure and I'm considering backing up differently too.
Up till now I back up all of my photography, pictures, office, movies separately, but the photog and pictures are huge folders, so they can take up to 6-7 hours each to backup.
Now that my file structure is root/year/month/subject, for each of the above, I'm thinking about backing up each month of the year separately from one another. The plus side I can see if once a month is backed up, you don't have to back it up again unless you make changes. The downside is if I have to ever go to the backups, I will have to restore each month separately. I use Genie Backup Manager and works very well.
I'm also wondering if backing up in smaller chuncks can preserve some data in case other data gets corrupt somehow.
So do you backup in small chunks which takes less chuncks of time, or do you backup everything at once and just let the computer run for what can be days.