Hello:
The IEEETran class has a corresponding LyX layout which seems to work well. 
Many theorem-like environments are provided in the drop-down "environment" list
on the top left corner.

But how can one choose per-section numbering (Theorem 3.5 for the firth theorem
in the third section, for example)?

According to the IEEETran manual, the newtheorem command allows for such
specification.

The user must first declare the structure name via
 
\newtheorem{struct_type}{struct_title}[in_counter]

where struct_type is the user chosen identifier for the structure, struct_title
is the heading that is used for the structure and in_counter is an optional name
of a counter whose number will be displayed with the structure number and whose
update will reset the structure counter.

Papers that use in_counter usually use “section” such that the section number is
the first part of each theorem number.

Example: \newtheorem{thm}{Theorem}[section]

It seems that LyX follows the same procedure when asked to generate LaTeX, but
ommitts the "counter" specifier (thus theorems are numbered sequentially
throughout the paper:

\newtheorem{thm}{Theorem}

The question is whether one can specify the counter (third parameter) from
within LyX, and how to do it.



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