and
Perhaps you could do sketch (even a hand drawn one) of how the UI might work in the scenario you are describing. I can’t see an easy way to distinguish between a primary annotation file and annotations files that relate only to a specific portion of text. Remember the URL field can only link to one document or group - this is the annotation document or annotation.
If you have many quotations that you want to link into a single file you can merge them afterwards simply by selecting and merging all the text files in the linked tag group. This has the advantage that your annotations can also be placed in the order you want them in the final text document before you merge them.
The next version of the “Make annotation files for each citation plus notes+tags” script will adopt the template model of DT’s existing annotation script so you will be able to choose what fields you want in the annotation.
Actually you can emulate something like this by highlighting the text, drawing a link box around it, and pasting the the url of the annotation into the url link of the link box. Its clumsy so wont work for anything other than the occasional annotation. Unfortunately I can’t see any way to automate it because there is no programmatic access to the pdf annotation tools.
As a matter of course I tend to highlight or mark with an adjacent red line any passage which I have annotated. Because I preface my annotations with a page number its generally no more than two clicks to go directly to the appropriate annotation from the page of the pdf (One click on the url link to open the tag group and a second click to open the annotation itself) I also keep my passage highlight colour and my annotation highlight colour the same for any particular passage. This also helps with quick visual linking.
On different annotation styles
I think the virtue of DT’s approach is the ability to adopt a style of annotation which works for you (see for example this thread - [url]"Highlights" app - export annotations to DEVONthink, etc.] ). Recently for example, and because the type of document being annotated, is not susceptible of easy contextual annotation, I have been clipping whole series of pdf pages as annotations. This way I can more easily have a summary of the relevant marked up pages in context.
There is a lot written on the web about how people use DT different annotation techniques in in their writing. I found this article by Steven Berlin Johnson particularly good http://www.stevenberlinjohnson.com/movabletype/archives/000230.html.
I also cannot commend Alex Strick’s recent post highly enough especially if you use a lot of kindle reference material - http://www.alexstrick.com/a-different-place/2014/10/note-taking-jujitsu-or-how-i-make-sense-of-what-i-read
Frederiko