How to handle only overlays while printing a latex beamer notes

Question

Using overlays and showing multiple graphs in the same slides and even text is really great but I am really wondering how can we show each piece of overlay while printing the slides or notes ? It seems some of the slide can have multiple pages in order to accurately show all the graphs and text especially when we use overlays such as \only<1-3 and \only<4-5>. If it is just a regular text and fills only one page then it should be fine. But often times it is more complex than that. Would anyone clarify what can we do under such circumstances ?

EDIT: MINIMAL EXAMPLE ADDED

What I mean here is that on the second slide I have three different tikz picture. Here I didn't include the picture on node (0,0). In my slide I am using the pictures. SO, how can I print all these three pictures on the same page ? In other cases also some of the text doesn't fit on the slides. I hope it is more understandable now.

A minimal working example

%\documentclass[mathserif]{beamer}

\documentclass[arial,handout]{beamer}

\usepackage{pgf,pgfpages}
\usepackage{graphicx}
%\usepackage{units}
%\usepackage[utf8]{inputenc}
\usepackage{mathtools}
%\usepackage{amsmath}
\usepackage{animate}


\usepackage{booktabs}
\usepackage{tikz}
\usetikzlibrary{arrows,shapes}

 \tikzset{
    invisible/.style={opacity=0},
    visible on/.style={alt=#1{}{invisible}},
    alt/.code args={<#1>#2#3}{%
      \alt<#1>{\pgfkeysalso{#2}}{\pgfkeysalso{#3}} % \pgfkeysalso doesn't change the path
    },
  }

\mode<presentation>
{
  \usetheme{ift}
  \setbeamertemplate{items}[square]
}

\usefonttheme[onlymath]{serif}
\setbeamerfont{frametitle}{size=\LARGE,series=\bfseries}

\definecolor{uibred}{RGB}{170, 0, 0}
\definecolor{uibblue}{RGB}{0, 84, 115}
\definecolor{uibgreen}{RGB}{119, 175, 0}
%\definecolor{uibgreen}{RGB}{50, 105, 0}
\definecolor{uiborange}{RGB}{217, 89, 0}

%% Create a new command called redub for underbraces
\newcommand\redub[2]{%
    \colorlet{currentcolor}{.}%
    \color{red}%
    \underbrace{\color{currentcolor}#1}_{\color{red}#2}%
    \color{currentcolor}%
}


%Beamer block template
\setbeamertemplate{blocks}[rounded][shadow=true]

\setbeamercolor{block title}{bg=uibblue,fg=white}
\setbeamercolor{item projected}{fg=white,bg=green}

\beamertemplatenavigationsymbolsempty


%\include{macros}

%\includeonlyframes{current}


\defbeamertemplate{enumerate item}{mycircle}
{
  %\usebeamerfont*{item projected}%
  %\usebeamercolor[bg]{item projected}%
  \begin{pgfpicture}{0ex}{0ex}{1.5ex}{0ex}
    %\pgfcircle[fill]{\pgfpoint{0pt}{.75ex}}{1.25ex}
    \pgfbox[center,base]{\color{uibblue}\insertenumlabel.}
  \end{pgfpicture}%
}
[action]
{\setbeamerfont{item projected}{size=\scriptsize}}
\setbeamertemplate{enumerate item}[mycircle]

\begin{document}

%\setbeamertemplate{background}
% {\includegraphics[width=\paperwidth,height=\paperheight]{slide_bg1}}
%\setbeamertemplate{footline}[ifttheme]

\mode<presentation>

\begin{frame}
    \frametitle{Eulerian Salt Flux Decomposition}

    \only<1-2>{\begin{itemize}
        \item Subtidal Volume discharge rate $Q_f$: through a cross=section A  \\
        $Q_f = \langle\int u.dA \rangle$
        \item Salt transport rate $F_s$ through a cross-section A \\
        $F_s = \langle \int uS.dA \rangle$
    \end{itemize}}
        \onslide<2->Sub-tidal salt flux decomposed into three parts 

    \onslide<2->\begin{align*}
        F  & = \langle \int(u_0+u_E+U_T)(s_0+s_E+s_T)dA \rangle \\
            & \approx \langle \int(u_0s_0+u_Es_E+u_Ts_T)dA \rangle \\
            & = \redub{Q_fs_0}{\mathclap{\text{     River flow     }}} + 
             \redub{F_E}{\substack{\text{Exchange}\\\text{shear dispersion}}} + 
             \redub{F_T}{\substack{\text{tidal osciallatory}\\\text{salt transport}}}
    \end{align*}

    \onslide<3->\begin{itemize}
        \item $u_0$ and $s_0$ tidally and cross-sectionally averaged
        \item $u_E$ and $s_E$ tidally averaged and cross-sectionally varying 
        \item $u_T$ and $s_T$ tidally and cross-sectionally varying
    \end{itemize}

\end{frame}

\begin{frame}
\frametitle{Age of Water under dye from all Rivers}

    \only<1-3>{\begin{tikzpicture}
    \centering
        \node [](0,0)(start){ hello2};
%       \draw [step=0.5cm,thin,dotted] (-5,-4) grid(5,4);
%       \node [circle]at (-4.5,0){0};
%       \node [circle,radius=0.9cm,fill=red!30,] at (-4.5,0)(a){};
        \draw [red,fill=red!30](-4.3,-0.2)circle(0.1cm);
        \draw [red,fill=red!30](-3.3,0)circle(0.1cm);
        \draw [red,fill=red!30](-2.5,-0.7)circle(0.1cm);
        \draw [red,fill=red!30](-4.,-0.8)circle(0.1cm);
        \draw [red,fill=red!30](-4.,-1.2)circle(0.1cm);
        \draw [red,fill=red!30](4.3,1.6)circle(0.1cm);
        \draw [red,fill=red!30](3.3,2.7)circle(0.1cm);
        \draw [red,fill=red!30](1.6,3.5)circle(0.1cm);
        \draw [red,fill=red!30](1.3,3.5)circle(0.1cm);      
        \node [rectangle,text width=4cm,red] at (5.5,3) (return) {$Q_2 = 169 A^{0.616}$     \linebreak Mason et. al. 1998};
        \node [rectangle,text width=4cm,red,visible on =<2->] at (5,0) (return) {Smaller near the source     \linebreak Increases away from the source};
        \draw [red,visible on =<3->](-3.3,-1.5) circle(0.7cm);%wolf bay small age
    \end{tikzpicture}}

        \only<4-5>{\begin{tikzpicture}
        \node [](0,0)(start){hello1};
%   \draw [step=0.5,dotted](-5,-4) grid (5,4);
     \node [rectangle,text width=4cm,red] at (5,0) (return) {Scale different from    \linebreak 2 year inflows};
     \node [rectangle, text width =4cm, red,visible on =<5->] at (5,-2) {Maximum age of 120 days};
     \draw [red] (1.5,-1) ellipse(1cm and 0.6cm);
     \node [rectangle, text width=4cm, red] at (5,3) {Minimum 7 day flow over 10 yr. interval};
    \end{tikzpicture}}  

        %
        \only<6-7>{\begin{tikzpicture}
        \node [](0,0)(start){hello};
        \node [rectangle, text width=4cm, red, visible on =<7->] at (5,3) {Mean inflows over 10 yr. interval};
        \end{tikzpicture}}
\end{frame}

\end{document}

Answer 1

Converting my comments above into an answer:

In specifying overlay options, you can add the handout:<number> option. For example, \only<1-3| handout:1>{content-1} will print content-1 that appears in frames 1 to 3 as the first page of the handout; \only<4-5| handout:2>{content-2} prints content-2 which appears in frames 4 and 5 as the second page of the handout; and \only<6-| handout:0>{content-3} will instruct beamer not to print content-3 that appears on frame 6 onwards. Notice that a space is needed between | and handout.

To not show an item/graphic in the handout, simply set handout:0.