Glad you got it sorted. Probably the last folder you opened or saved-to was the Download folder.
I just have a megafolder called Online (because it started as my working folder for building websites). Beneath that is a folder called Books, and beneath that is a folder for each book. So whatever I am working with -- Sigil, Word, OpenOffice Writer, DOS Wordstar, Photoshop -- I go to the same spot.
A great thing about Sigil is that, unlike every other software I've worked with, it has an option to Save A Copy. As long as the program stays open (which for me is often days at a time) it will put that Copy into my Dropbox folder. And I never confuse the working version with the Copy version. Every other program requires that I Save As, so I have to remember whether I am working in Dropbox or in Online/Books/ThisHereBook.
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