This information @lubos told me long ago may help you understand what happens:
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00000000-0000-0000-0000-000000000000.manager is an index file. It stores a list of businesses you have. In case of the server edition, it also stores a list of users and other information. It doesn’t contain any accounting data.
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The second file with the long, alpha-numeric title should be your accounting data. This should be the biggest file. If you have more than one business, there will be more files with similar type names.
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The data file contains the path to your accounting data, telling Manager where to look. If you move and/or delete the data file, a new file will be created at the default location. Manager will look for this file to see where to probe for your data.
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The size file contains height and width of Manager’s window when it was last closed. So when you open Manager next time, your window size is the same as last time. So that file will show having been modified every time you close, even if nothing was done.