Posting this information in case it helps someone else.
When moving up from a previous version of RoboHelp and using FrameMaker files, the following works to use your .css file to apply your formats. Your .css file needs to be sitting in the contents > assets folders.
First, search and replace in your .css file so that the format of a tag is p.bullet or p.heading1 for example. Mine differed, so search and replace fixed the formats.
Set the Project Settings and each file to use the .css file. (Not sure what Project Settings does here. It seemed to do nothing.) Setting each file to use the .css file fixes the display in RoboHelp. (I had to redo this for each file after updating the book/files.)
Set the Master Page to use the .css file. As another post noted, the Master Page overrides everything else. Setting the Master Page fixes the display in the output.
Based on my initial experience, this is what has worked so far.