There’s a couple things you can do to facilitate note taking in an RTF document.
Keyboard shortcuts for headings:
There’s a few steps you need to do to set this up. First, make sure the formatting bar is visible (Format > Show Format Bar). This is the standard TextEdit format bar, and you can use it to save and name some key styles (e.g. I have Title, Heading, Normal). Then you can use the OS Keyboard Shortcuts tool to make, well, keyboard shortcuts.
- add a shortcut for DevonThink3
- in Menu Title, put the name of the saved style (make sure that your name doesn’t conflict with an existing menu command, or it won’t work)
- in Keyboard shortcut put the keycommand you want

Shortcut for bullets
Similar to above, but you don’t need to make a style for it. The Format bar already has a menu for different kinds of bullet lists:

You just need to create a Keyboard Shortcut that bullet style. So for a traditional bullet list, this is what the keyboard shortcut looks like:

(You make the bullet character by pressing option-8). I then did another keyboard shortcut to turn bullet lists off, which is called “None” in the menu:

Outline mode
Well, I just made an applescript that sorta-kinda mimics this. I make all of my headings bold text (major headings are also all-caps). So this script will make a list of all paragraphs that are entirely bolded, and ask you to select one — it will then jump to that position in the document.
Save that script in the Toolbar subfolder of the Scripts menu, the customize your toolbar, and you’ll have that tool once click away.
FAIR WARNING: it is slow, and while it works for me, I am not an expert at applescript, so use with caution.