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Let me profess that I know that I have made some bad choices. Hopefully I can get some help here, to clear things up. I have been told and read that writing an article/paper should in most cases be done in the document class memoir, for being the most flexible and with the most tools.

Now... I found this great template, which is written in the documentclass paper, which looked liked it only needed very few adjustments, to be really useful for my purpose, which I hope to use and share as a template at my faculty. Unfortunately I can't find any guide or notes about the documentclass paper, which is why I'm here to get help.

The preamble looks like this:

\documentclass[a4paper, english]{paper} 
\usepackage{lipsum, babel}
\usepackage[utf8x]{inputenc}
\usepackage[margin=2.5cm]{geometry}
\usepackage{graphicx}
\usepackage{xcolor}
\usepackage[colorlinks=true]{hyperref}
\renewcommand{\thefootnote}{\arabic{footnote}}
\usepackage{tikz}
\bibliographystyle{vancouver}
\usepackage{usebib}
\bibinput{bibliography}
%------------------------------------------------------------------------
\title{VERY LONG TITLE}
\subtitle{The subtitle\\
\hfill\includegraphics[height=3cm]{frog.jpg} %logo
\vspace{-3cm}}
\author{First Name (A) Last Name (A)\footnote{E-mail: A@university.com}\\
First Name (B) Last Name (B)\footnote{E-mail: B@university.com}}
\institution{Name of University}

Which produces something like this:

enter image description here

My first question is, why isn't the footnote for the authors e-mail showing up at the bottom of the page? (And how to fix this)

My second question is related to \checkandfixthelayout in memoir. Is there something similar for paper or is there another way to fix words exceeding the margin, as shown here:

enter image description here

So my big question is, if it's easier to make these few adjustments in paper, or to switch to memoir and build a similar setup? (and if so, how to do it.)

EDIT: Added the \usepackage{microtype} to the preamble, which has fixed the problem with the margin.

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    You found a template named paper? Where? – user31729 Feb 17 '16 at 18:11
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    Use \thanks instead of \footnote in the \author field to get the emails displayed at the bottom. As for the fix with words exceeding the margin, I'd recommend using the package microtype, at least as a first measure. – sodd Feb 17 '16 at 18:12
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    Regarding tho \checkandfixthelayout option, did you try to load the package microtype? I.e. simply add \usepackage{microtype} to your preamble. – Clément Feb 17 '16 at 18:12
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    i've just done a ctan search for anything named "paper", and the only plausible offering is a documentclass based on article, which bears absolutely no similarity to what you show. so we really do need to learn where you found this package before we can make any intelligent suggestions. – barbara beeton Feb 17 '16 at 18:39
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    Asking what is better, using memoir or using paper is a question very hard to answer. It is like asking which religion is better than another. You can savely try out both and decide which one fits you better. You also don't have to stick with your decision, you can later convert to another class ;-) – Johannes_B Feb 17 '16 at 19:08
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Exceeding phrases over the margins can be fixed manually by either rephrasing or telling latex to individually hyphenate words con\-sti\-tu\-tion for example creates points to hyphenate.

Another method is to use the package \usepackage{microtype} to make microadjustments to your document. It changes things like interletter spaces etc. Usually the default settings might be enough (I used it for easing the bibliography that went over the margins in my phd). However, more indepth adjustments can be made, some of which change the face of your document however -- so you have to decide if you can live with that.

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