If you want both the decimal and the integer part in groups of two that can be done with the options digit-group-first-size=2, digit-group-other-size=2. However, if you want different grouping for the two parts then need a macro that seprates the integer and decimal parts and applies the desired settings to both parts:

Code:
\documentclass{article}
\usepackage{siunitx}
\usepackage{xstring}
\makeatletter
\newcommand{\numI}[1]{%
\StrBehind{#1}{.}[@DecimalPart]%
\StrBefore{#1}{.}[@IntegerPart]%
\num[
digit-group-first-size=3, digit-group-other-size=3,
]{@IntegerPart}%
\num[
digit-group-first-size=2, digit-group-other-size=2,
]{.@DecimalPart}%
}
\makeatother
\begin{document}
$\numI{123456789.123456789}$
\end{document}