\input and \include for a thesis

You should input your .tex files in this way:

\documentclass[options]{theclass}

%preamble

\begin{document}
\section{section1name}
\input{sec1} %the file is sec1.tex 

\section{section2name}
\input{sec2} %the file is sec2.tex
.
.
.
\end{document}

So latex will paste the text where you call \input{}

include works quite the same but it starts a new page when you call \include{}

That would be the best strategy.

If you want just one file, then write the document in this way:

\documentclass[options]{article}

    %preamble

    \begin{document}
    \section{section1name}

    Write your text as 
    I am writing 
    write your text...

    \section{section2name}

    Same way 
    .
    .
    .
    \end{document}

As you can see, both cases have just one begin-end document.

If you want to avoid numbered sections use the starred command

\section*{}

The difference between \input and \include is how it's included, there is an old discussion on how to use them.

No, you do \begin{document} things only once. Then you use \include{chapter3} once per chapter. You can basically cut the chapter text from the big document, place it into chapter3.tex and insert the include statement instead in the main document.

Update: Oh, an continuing scrying into your question: you compile the main document, as before. As the start of the compilation regarded, nothing changes for you that multiple included *.tex files are present.

I also recommend latexmk and git for more easy compilation and management of the source, but that's tangential.