I wonder if there is a way to create an equation like that where the "subscript" is placed underneath instead of in the bottom right corner. I also want the "subscript" to be center aligned with the number above.

I wonder if there is a way to create an equation like that where the "subscript" is placed underneath instead of in the bottom right corner. I also want the "subscript" to be center aligned with the number above.

A simple realization is with amsmath and \underset:
\documentclass{article}
\usepackage{amsmath}
\begin{document}
\[
y=\underset{(20)}{35}\cdot x + \underset{(3)}{39}\cdot z + \underset{(11)}{3859}
\]
\end{document}

However, you see that the first pair is perhaps too wide, because the subscript width is taken into consideration. If the subscript is never much wider than the number, you can use also \mathclap from mathtools; with a new command also the syntax is handier.
\documentclass{article}
\usepackage{mathtools}% also loads amsmath
\newcommand{\twonums}[2]{\underset{\mathclap{(#2)}}{#1}}
\begin{document}
\[
y=\twonums{35}{20}\cdot x + \twonums{39}{3}\cdot z + \twonums{3859}{11}
\]
\end{document}

\undersetfromamsmathdoes just this. – egreg Apr 06 '13 at 14:15