@Jerome Thanks for the reply and all seems to be working fine with DSE except for the help file not opening up and definitely will always try to remember to quit DSE between sessions.
It seems like you are having the same issue with the help file not opening up in DSE which I also posted about at: Dramatica Story Expert Getting Started Window Problem.
Interestingly, looking through ‘file:///Applications/Dramatica Story Expert/Help/index.html’ file and the parent folder it seems that the same information is available from DSE Documentation.
I believe this DSE help manual was built using the Help+Manual app so maybe like what you were saying there is an incompatibility with Help+Manual and El Capitan, but it would be a nice feature to be able to access the help file within the app and not have to open up another document.