For the two-body problem, assuming the bodies have respective masses $m_0$ and $m_1$, with respective positions $𝐫_0$ and $𝐫_1$, and assuming there are no forces at play other than their mutual gravity, the equations of motion are:
$$\begin{align}
𝐩_0 &= m_0\frac{d𝐫_0}{dt}, &\quad \frac{d𝐩_0}{dt} &= \frac{Gm_0m_1}{|𝐫_1 - 𝐫_0|^2}\frac{𝐫_1 - 𝐫_0}{|𝐫_1 - 𝐫_0|},\\
𝐩_1 &= m_1\frac{d𝐫_1}{dt}, &\quad \frac{d𝐩_1}{dt} &= \frac{Gm_1m_0}{|𝐫_0 - 𝐫_1|^2}\frac{𝐫_0 - 𝐫_1}{|𝐫_0 - 𝐫_1|},
\end{align}$$
where $𝐩_0$ and $𝐩_1$ are their respective momenta.
Under the conversion:
$$\begin{align}
𝐏 &= 𝐩_0 + 𝐩_1, &\quad M &= m_0 + m_1, &\quad 𝐑 &= \frac{m_0𝐫_0 + m_1𝐫_1}{m_0 + m_1},\\
𝐩 &= \frac{m_0𝐩_1 - m_1𝐩_0}{m_0 + m_1}, &\quad m &= \frac{m_0m_1}{m_0 + m_1}, &\quad 𝐫 &= 𝐫_1 - 𝐫_0,
\end{align}$$
the system reduces equivalently to:
$$\begin{align}
𝐏 &= M\frac{d𝐑}{dt}, &\quad \frac{d𝐏}{dt} &= 𝟬, \\
𝐩 &= m\frac{d𝐫}{dt}, &\quad \frac{d𝐩}{dt} &= -\frac{GmM}{|𝐫|^2}\frac{𝐫}{|𝐫|}.
\end{align}$$
It's the full distance $𝐫 = 𝐫_1 - 𝐫_0$, but with the reduced mass $m = m_0m_1/(m_0 + m_1)$ for the orbiting body, and the total mass $M = m_0 + m_1$ for the body being orbited.
As a set of second-order equations, this can also be rewritten as:
$$\frac{d^2𝐑}{dt^2} = 𝟬, \quad \frac{d^2𝐫}{dt^2} = -\frac{GM}{|𝐫|^2}\frac{𝐫}{|𝐫|},$$
which underscores that it is with the full distance $𝐫$ for the orbiting body and the total mass $M$ for the body being orbited. When written in this form, the reduced mass $m$ drops out of the picture.