I use Quicken for Windows. I use four separate Quicken files: one for my family's finances, one for the finances of an estate for which I am the executor, and two for nonprofits for which I am treasurer. Until just now, I have had a separate folder for each Quicken file Family.QDF, etc.. Call the folders Family, Estate, NP1, and NP2. The automatic backup files, I then hoped, would be stored in folders Family\Backup, Estate\Backup, NP1\Backup, and NP2\Backup. However, that isn't what happened. The backups for Family.QDF might be stored in any of the Backup folders. I couldn't explain that.
Now I think I know what is happening. Can anyone confirm this: After opening one of the Quicken files, I would go to Edit→Preferences→Backup, where i could Open or Change the backup directory. I discovered that, regardless of which Quicken file I had opened, the settings were the same. In other words, if I opened the backup directory, it would show the same directory regardless of which Quicken file I had opened. That suggests that the backup preferences are associated with the installation of Quicken on my computer, not with each separate Quicken file.
Based on this, I have moved all four Quicken QDF files (Family.QDF, etc.) into a single folder called Quicken, which has a subfolder Quicken\Backup in which backups of all four Quicken files are stored. This seems to work.
A related annoyance: Before consolidating the files and backup folders, I noticed that I had several nested backup folders, e.g. Family\Backup\Backup. This seems to be because when you change the location of the Backup folder, you are meant to select the folder in which Quicken will create a Backup folder, not the backup folder itself, even though the text in the dialog box says "Browse for automatic backup folder…" However, confusingly, if you ask to open the backup folder, you will open the backup folder itself. Can anyone confirm this behavior?