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Actually, we do not yet have text annotations and I am not too sure weber we will include them in a future version. However, what you can use is several things: For just marking a position in the text, you can always use bookmarks. To write some annotation inthe text, you might also try to use either a paragraph or a dedicated inline style which can then be searched for and easily deleted during export.
This will be a VERY big change in Ulysses. We have this on our list like forever (okay - or when we first sipped it seven years ago, which feels like forever). There is a lot of conceptual stuff that needs to be worked out for this to work. We will give this a bump on our priority list. But given the complexity (like think of the things you might USE such a link for and implement that as well) I'm sure this is rather a 2.5 or 3.0 feature kinda thing. As we're planning several other things to do with the notes, this might actually become a quite interesting makeover.
Well, what you could do already is to use the shortcuts to navigate between the editor and the notes pad, as well as the shortcut to create a new note.
Think what would be the best is to have a annotations-notes link that resides in the counting column just like the bookmarks. In-line annotations that require clicks and stuff might not be too optimal. But we'll have to think. Don't expect it for 2.1.
Thinking about Xcode code folding bubbles right now. If you don't know what this is, don't bother. Just thinking...