Hi, Tim. Yes. Give the PDF its own document and take notes either in the Info panel Comment field or in a rich text page.
That’s really not all that limiting. Here are my tricks for making it convenient.
 Set up DT Pro’s windows so that the Info panel is always open and the Comment field is available for note entry whenever a document is selected or opened. If one of your databases has been designated as default using File > Database properties and Preferences has checked the option to remember the windows that were open when the database was last closed, this works beautifully. See a JPEG of my setup at http://homepage.mac.com/WebObjects/FileSharing.woa/wa/default?user=wbdeville&templatefn=FileSharing5.html&xmlfn=TKDocument.5.xml&sitefn=TKSite.2.xml&aff=consumer&cty=US&lang=en.
The name of the picture is “Modified Vertical Split.jpg”, but it works equally well if the view is switched to “Three-Pane” or “Column”. Both my MacBook Pro (15") and Power Mac (24") are permanently set up this way.
I usually note the page number in the PDF document when I make a note.
The disadvantage of the Comment field is that it is plain text only and cannot include character formatting or hyperlinks. So I actually do most such note-taking in the following way.
 I prefer taking notes in rich text, as that can have formatting and hyperlinks. In the simplest approach, create a new DT Pro rich text document, set a convenient width and place it to the right of the PDF page. I usually give such a notes document a name very similar to the name of the PDF, so that a Name search on either will pull the related document. Often, my notes document will contain a hyperlink to the PDF.
Most of the time I use a variation. Thanks to Alexandria for calling to my attention to the free utility called Afloat. This lets one designate a window in any application as “floating” above all windows, regardless of the application. Afloat also lets this window become almost invisible when the cursor is moved off it. Therefore, one can read “through” the floating window very easily. Such a floating window can be minimized to the Dock, where it’s available whenever needed.
I’ve got a daily journal/general notes DT Pro rich text document that’s open at all times. Using Afloat, I set it as “floating” and nearly invisible. At any time I need to make a note, whether in DT Pro or another application, it’s available in the Dock. When finished with it, minimize it by pressing Command-M.
When I’m collecting draft material and reference citations into Papyrus for final polishing, I’ll make my Papyrus document the only open one in Papyrus and set it as a floating, nearly invisible window. So I can select and drag text or images into Papyrus from DT Pro, or jump back to DT Pro to check for information in the database. Press Command-M while the Papyrus window is visible and it’s minimized. As DT Pro is “beneath” Papyrus, a click in a DT Pro window shifts the focus to DT Pro.
The same approach works with other word processors and makes such interactions almost as seamless as though the word processor were the native editor in DT Pro. I use the hybrid PDF file format in Papyrus 12, because such documents stored in DT Pro are directly editable by Papyrus.