@Herndz: Welcome to Mobile Read.
You really could be "cutting off your nose to spite your face" here.
http://en.wikipedia.org/wiki/Cutting...spite_the_face
Calibre is such a useful and flexible eBook Manager that I would suggest you persevere for a while before giving up on it. Have a look at
http://calibre-ebook.com/about and then play with its feature for a while.
Calibre as an eBook library manager is so flexible that you'll quickly realise that the internal folder structure is irrelevant – you never need to access the folders from your OS, it's all handled within calibre.
If you really want a specific folder structure on your device then you can use the send-to-device template; and for a structure on disk use the save-to-disk template.
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I do understand how it works now, I enter the strings in the Save to Disk area, but the ebooks keep coming out as though I changed nothing (even though I applied the changes).
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This comment suggests that you DO NOT understand how it works. Of course the ebooks keep coming out the same. The template DOES NOT affect how the ebooks are named on conversion. (it's not supposed to!), but only comes into play when you send-to-disk or send-to-device.
Give calibre a thorough test for a few weeks and you may well find that, like so many of us have already found, calibre becomes an indespensible eBook management tool.