Dear Richard and other LyX Users, I managed to solve a few of the formatting problems. To change the section labels from numbers to letters, I added the following to the nih.cls file:
\def\thesection{\Alph{section}} That solved the output problem. Now I am trying to get the labels for section, subsection, and subsubsection to match the LaTeX output. I've been able to figure it out for section: Style Section LabelType Counter LabelCounter section LabelString "\Alph{section}" End But I've been stumped on how to do the same thing for subsection and subsubsection. This still show 1.1 and 1.1.1 respectively, but only in LyX. The LaTeX output is correct. Cheers, Rob