@Dastral - firstly, don't ever give up on using series metadata
. You can use Metadata plugboards to manipulate the metadata when you export books out of calibre (I know nothing about an Aldiko reader, but I am sure you could either use a filename template or a metadata plugboard to insert series into your title). The Kindle doesn't support series info either, but metadata plugboards are how we get the titles to display with series info in them. See the library subforum for the stickies. If you need help setting it up just post in that Library Management forum.
Once you do that, you should find producing the covers you want much easier. And you will not have issues with other plugins or features in calibre which expect series information to be in the series column, not in the title.
So I think that just leaves your question about right margins - I'll add your request for it to the list for the next release.