As Harish explained, a matrix offers two layers (inside nodes and matrix) but both are drawn on main (default) layer. backgrounds library introduces two more layers background and foreground. But if you need more layers you can define them with \pgfdeclarelayer and once declared order them with \pgfsetlayers command.
Next code based on Harish example shows how to use both commands.
\documentclass[10pt]{article}
\usepackage{tikz}
\usetikzlibrary{fit,matrix}
\tikzset{
bigbox/.style = {draw=blue!50, thick, fill=blue!10, rounded corners, rectangle},
box/.style = {minimum size=0.6cm, rounded corners,rectangle, fill=blue!50},
}
\pgfdeclarelayer{background}
\pgfdeclarelayer{foreground}
\pgfdeclarelayer{minusone}
\pgfdeclarelayer{minustwo}
\pgfdeclarelayer{minusthree}
\pgfsetlayers{minusthree,minustwo,minusone,background,main,foreground}
\begin{document}
\begin{tikzpicture}[outer sep=0.05cm,node distance=0.8cm]
\matrix (a)[row sep=2mm, column sep=2mm, inner sep=2mm, bigbox, matrix of nodes, every node/.style=box]
{
1 & 2 & 3\\
4 & 5 & 6\\
};
\matrix (b)[row sep=2mm, column sep=2mm, inner sep=2mm, bigbox, matrix of nodes,
every node/.style=box,anchor=west] at ([xshift=2cm]a.east) {
1 & 2 & 3\\
4 & 5 & 6\\
};
%
\begin{pgfonlayer}{background}
\node[bigbox,draw=red,fill=red!10] [fit = (a)] (A) {};
\node[bigbox,draw=red,fill=red!10] [fit = (b)] (B) {};
\end{pgfonlayer}
\begin{pgfonlayer}{minusone}
\node[bigbox,draw=green,fill=green!10] [fit = (A) (B)] (AB) {};
\end{pgfonlayer}
%
\begin{pgfonlayer}{minustwo}
\node[bigbox,draw=purple,fill=purple!10] [fit = (AB)] (AB-1) {};
\end{pgfonlayer}
\begin{pgfonlayer}{foreground}
\node[bigbox,draw=orange,fill=orange!10,opacity=.5] [fit = (a-2-2.west|-AB-1.south) (b-1-2.east|-AB-1.north)] (AB-2) {};
\end{pgfonlayer}
\begin{pgfonlayer}{minusthree}
\node[bigbox,draw=brown,fill=brown!10] [fit = (AB-2) (AB-1)] (AB-3) {};
\end{pgfonlayer}
\end{tikzpicture}
\end{document}
