I was an early adapter of Manuscripts, but I must say that this software has not lived up to its promise at all.
The latest problem is the 1.2 update, and the latest beta version which I keep getting prompted to install. The add has been unusable entirely for me since 1.2 became available, even before MacOS Sierra was released. Since then, the latest beta version simply will not install ("unexpected error") and when I follow the instructions to download the latest version from the website the same thing happens.
Bibliography formatting remains an issue as posted elsewhere i.e. some listing are still appearing on an unexpected new line...
Smith et al. The Lancet etc etc
Rogers et al. Nature etc etc
I have attempted to write an article using manuscript several times only to run into so many formatting issues and crashes as to need to abandon using it and switch back to using Word with Papers.
Despite good communication in the forum here, nothing seems to be improving, so unless the major problems (formatting, crashing, problems updating) don't resolve, I'll be abandoning Manuscripts forever. Note that as the resident tech-head in a department of entirely non-tech colleagues, I've convinced literally dozens of people to buy Papers - right now, I will NOT be recommending Manuscripts.