I'm writing my thesis, and I have (only) two questions:
1. I need all the pages of the Intro (index, etc) numbered with roman (not Roman) centered in the bottom of the page, and the rest of the document (starting in \mainmatter) numbered with arabic in rigth position, top of the page. How could I do this??? I already know how to switch between roman/Roman/arabic, and I've tried something like this (but doesn't work):
and switching the \thepage, but it doesn't work (all the text results with the same first number position).
2. The chapters must be numbered with Romans (not roman), but within the sections, in arabic: (for example):
IV. Chapter 4
4.1. Section 1 (of the chapter 4)
4.1.1. Subsection…
4.1.1.1. …
You can customize the layout of the header and foot line with the fancyhdr package. I believe you could change the layout at anytime (check the documentation).
This *.pdf is a nice compilation which contains general hints on formatting...
To answer a question like this, we need more information, such as what document class you're using, and so on. What would really speed things up is to provide a minimal working example we could modify to make work.
I do wish you had clicked the link I had given describing how to construct a minimal working example. A minimal example is just that: minimal. It shouldn't load packages and include commands that have nothing to do with your question. More importantly, it shouldn't use \include or \input commands to include subdocuments that others do not have access to. What is someone supposed to do with your code when it cannot be compiled? How is someone supposed to answer your question when they don't know how commands in those subdocuments might affect the situation? See the Post on Avoidable Mistakes.
Hence, what I have below is mainly just a guess about what you may want.
Some observations:
On a mac, it's unlikely that you should be using latin1 encoding; it's more likely that you're using UTF8 (Unicode).
You load the graphicx package twice. Take out the second call to it. These days it's usually better to let the driver (pdftex) be automatically detected rather than load it as an option.
You're loading both titlesec and fancyhdr, two different packages that affect headers and footers. You should choose one or the other and stick with it. Since the commands you mentioned are titlesec commands, perhaps we should stick to those.
The \frontmatter command automatically makes page numbers roman style, so you don't need to explicitly turn that on. The \mainmatter command automatically resets the numbering to 1 and switches to arabic numbers, so there's no need to manually do this.
Normally, plain style is only used for the first page of a chapter, so if you want it for every page, you need to use the \pagestyle{plain} command; you had, but I think you needed to re-do it after \mainmatter.
Below is some sample code that as far as I can tell produces the desired result. (Note that the lipsum package and \lipsum commands are not part of the solution, but are just there to produce filler text.)