… I then used PDFClerk and set the imposition to two pages per sheet side with the idea to create a nice booklet.
However, after printing duplex I found out that when turning a page the backside was upside down! What did I mis?
Welcome Dreeke,
Since you do not mention any pages being upside down on-screen I will assume everything looks hunky-dory on-screen and the issue is solely to do with the way the printer works. Let me know if this is incorrect.
If your printer requires manual duplexing it is possible that you when you flipped the pages over to print the back sides you fed the paper with the wrong end first. Print the batch again and when printing the back sides make sure you feed the paper rotated 180° compared to how you fed it the first time. If you don’t remember which way you fed the paper, print the first side of sheet 1 (by setting the print dialog to print only page 1). Then flip the resulting sheet of paper over and feeding it to the printer for printing the backside of the sheet (setting the print dialog to print only page 2). Remember the orientation in which you fed the paper to the printer. If the second side comes out upside down you know you will need to feed the paper the other way around. Once you get the desired result you can safely print the whole batch.
If you printed with automatic duplexing then you may have chosen the wrong binding edge in the print dialog. For the 2-up layout you most likely need to choose short edge binding. Depending on your printer model the duplexing options can be in different subpanes of the print dialog, so you may have to look around to find it.
If none of the above works or is an option then, in PDFClerk 2.5 and up you can easily flip all backside pages in the document upside down so that they come out correctly when printed. For this select page two in the page list, then control-click (or right-click) the list and choose “Select Alternating Pages” from the contextual menu. Then rotate the selection right [Tools->Rotate Right ⌘R] twice to flip the even pages. (In older versions of PDFClerk you can still rotate the pages, but you will have to manually select all the even pages.)