Jon, first, thanks so much for taking the time... I don't know how you do it.
I have created several custom formats (for different publishers etc.) with changes for first and second plus citations etc.. My question concerns formatting within the one custom format. As far as I can tell, under format manager, I can choose either Author, A.B., OR A.B. Author such that after running a scan I get my footnotes (= citation, right?) and appended bibliography in which ever one of those options I choose. But I'm wondering how in the same custom format (i.e. for the one publisher) I can have my footnotes (citations) A.B. Author, and my appended bibliography, Author, A.B. I think I've read the Guide fairly carefully but still can't see how to do this. Are you suggesting that I need two custom formats for the one document—one for the citations and another for the attached bibliography? Is that possible? If I've missed something, please don't bother explaining it (that will waste your time), just send me the page numbers in the Guide and I'll check it out.
The "master" format is in control of the bibliography. So you'd set the author output to surname first. In the Bib & Citations tab of the format, you'd set "Citations" to "custom citation format", and from the popup menu select the format you want to control citations (footnotes in your case, but they can be in the body of the text, too).
In the custom citation format you tell Bookends to output authors surname last.
When you do the scan, you'd select the "master" format to scan with. It would call the custom format when it ran into citations. See?
If there are still some problems, please contact me directly and send me your two formats (zipped, please) and I'll see if they are configured properly.
Very simple. All I needed to do was make a copy of my publishers format, label it "publisher citation," make the changes to that, and use it as my custom citation format in the "master" publishers format. Brilliant.