Point at other parts of the PDF

Typing “see Figure 3” by hand is a promise you cannot keep. Add one figure earlier in the paper and every hand-typed number after it is wrong. LaTeX solves this with a two-part mechanism: \label attaches a name of your choosing to a numbered thing, and \ref prints whatever number that thing ended up with. You refer to names, and the compiler keeps the numbers honest.

Label and ref

\section{Methods}\label{sec:methods}
\begin{equation}\label{eq:main} ... \end{equation}
\begin{figure}
 ...
 \caption{...}\label{fig:pipeline}
\end{figure}

See Section~\ref{sec:methods}, Eq.~\eqref{eq:main}, and Figure~\ref{fig:pipeline}.

\label{sec:methods} records the most recently assigned number, here the section’s, under the key sec:methods. Later, \ref{sec:methods} prints that number, and \eqref is the amsmath variant that adds the parentheses convention for equations, printing “(1)” rather than “1”.

Two details in this example are load-bearing. First, inside a figure the label must come after \caption, because the caption is what steps the figure counter; a label placed before it silently picks up the current section number instead. Second, the ~ in Figure~\ref{...} is a non-breaking space, which keeps the word and its number on the same line rather than letting “Figure” end one line and “3” start the next.

The sec:, fig:, and eq: prefixes are pure convention. LaTeX does not require them, but they make keys readable and let editor autocomplete group your labels by kind.

Why you see ??

On the first compile after adding a label, \ref prints ??. Numbers are resolved through the .aux file written during the previous run, so a new label needs one more compile to appear; why you compile more than once explains the mechanism. A ?? that survives two consecutive compiles almost always means the key in \ref does not match the key in \label.

cleveref writes the word for you

With cleveref (load after hyperref):

\usepackage{cleveref}
\cref{fig:pipeline}

\cref{fig:pipeline} prints “Figure 3”, the type name included, and adapts if the label turns out to be a table or an equation instead. \Cref capitalizes for sentence starts, and \cref{eq:a,eq:b,eq:c} compresses a list into a range. Note the load order: cleveref is one of the few packages that must come after hyperref, the reverse of the usual rule. Adopt it early, because retrofitting \cref into a paper full of hand-written “Figure~\ref” phrases is tedious.