This is something which has bugged me for a while, and I finally did something about it.
There's a new option when exporting/printing now - Presets. You can create presets where you define which chapters are included when exporting, by dragging and dropping titles between two lists on the new setup form. Then you save the preset with a name, and when you print or export you can pick the preset.
So, for example, you could include three novels in the one yWriter project, keep the same header and footer pages where appropriate (e.g. 'about the author'), and then create export/print presets which would only export the relevent chapters for each book.
I'm still fine-tuning this new feature, and will release a beta soon.
PS I released the ebook edition of Hal Spacejock 6: Safe Art yesterday, and Hal 7 is going to be a serialised novel which is why I had to do something about custom exports!
Cheers
Simon
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Spacejock Software:
http://www.spacejock.com
Hal Spacejock:
http://www.spacejock.com.au/HalSpacejockSeries.html
Hal Junior (8-12):
http://www.haljunior.com