I recently purchase a copy of Manuscripts having used the trial for a while. I love the layout and usability of the application but in its current form, using it to write scientific documents for submission is too complex to use regularly. My experience is that you can use it to generate LaTeX but then need to edit the LateX to enable submission to journals. Haven't seen a significant update for quite some time and no real feedback about the development of the application so committing to it is difficult.
Examples of shortcomings include:
Can't cross reference to sections in the text
Can't insert equations into tables, labels
Can'\t change how equations are referenced in the text (equation (1) is often not needed, just (1))
Can't make/customise section headings roman, etc.
Can't have multi-column output
Can't have N stacked figures (where N=5,7, etc)
Not sure how to separate appendix numbering.