I haven't had the time to confirm what magic makes this work, but I've got SharePoint and Adobe playing well with each other.  I'm using SharePoint 2003 and Adobe Acrobat 7.0 Professional. I can now:

1. check out a PDF file
2. Edit it in Acrobat (by choosing "Edit in Adobe Acrobat" from the drop down menu in the document library)
3. Save it (back to the document library)
4. check it back in

This is all just like the way it works in Word, Excel, or PowerPoint.

First, begin following the directions in KB article 837849, then when you're at step 2b, add the following text inside Mapping XML element: 

EditText="Adobe Acrobat" OpenControl="SharePoint.OpenDocuments"

so that the entire element looks like this:

<Mapping Key="pdf" Value="NameofIconFile.gif" EditText="Notepad" OpenControl="SharePoint.OpenDocuments"/>