Actually, never mind; empheq is overkill for what you need, and hard to use in
LyX.  Just insert a parbox with a frame, and put the equation array inside the
parbox.  I've appended a small example below.


#LyX 2.0 created this file. For more info see
\lyxformat 413
\textclass article

\use_default_options true
\maintain_unincluded_children false
\language english
\language_package default
\inputencoding auto
\fontencoding global
\font_roman default
\font_sans default
\font_typewriter default
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 100

\graphics default
\default_output_format default
\output_sync 0
\bibtex_command default
\index_command default
\paperfontsize default
\spacing single
\use_hyperref false
\papersize letterpaper
\use_geometry true
\use_amsmath 1
\use_esint 1
\use_mhchem 1
\use_mathdots 1
\cite_engine basic
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
\use_refstyle 1
\index Index
\shortcut idx
\color #008000
\leftmargin 1in
\topmargin 1in
\rightmargin 1in
\bottommargin 1in
\secnumdepth 3
\tocdepth 3
\paragraph_separation skip
\defskip smallskip
\quotes_language english
\papercolumns 1
\papersides 1
\paperpagestyle default
\tracking_changes false
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false


\begin_layout Standard
Some boxed equations:

\begin_layout Standard
\align center
\begin_inset Box Boxed
position "t"
hor_pos "c"
has_inner_box 1
inner_pos "t"
use_parbox 1
use_makebox 0
width "25col%"
special "none"
height "1in"
height_special "totalheight"
status open

\begin_layout Plain Layout
\begin_inset Formula 
y & = & mx+b\\
z & = & \int_{a}^{b}f(\tau)d\tau






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