I am very new to Mathematica but see its potential. I'm unsure of how to combine text and Mathematica computations in a notebook so that the final document reads properly, and I haven't found a tutorial or any other help that covers this. A near as I can make out, one writes the document as if it were an ordinary word processing document, interspersing Mathematica calculations and commands, and then one collapses the cells that one does not want to display in the final document. Is this correct?
What I'd like to do is to adopt certain notational conventions and have mathematica deal with them correctly. For example, one set of conventions italicizes names of all variables, uses uppercase letters to name random variables and matrices, but distinguishes random variables from matrices by displaying all matrix names in boldface. A different set of conventions will use italicized uppercase letters to designate points in a diagram or constant parameters in an equation, with matrices now designated as uppercase letters with the dimensions of the matrix as a subscript (e.g., n x m).
Ideally, one would have a mathematical style sheet that makes changing the conventions used in a document. But even if one were to be willing to use a fixed notation in a document (notebook), I'm not sure how it would work. How does one use X to designate a random variable and bold X to designate a matrix? How does one use the Greek letter pi as a variable and have it show up in the document as the Greek letter rather than as the word "pi"?
So what's the best way to deal with these issues?
The question you are asking has been many times addressed in this forum. I would encourage you to look up the archive. I collected some of the subjects close to your question that were discussed during last 2 years, which may help you to find at least some of them. Here they are:
Using a notebook - how to add a caption and
Using hyperlinks to move to computations and back to text
Resources on using stylesheets for publishing
How to lock down a Dynamic object in a report
creating a graphic in a text cell
Typesetting in Mathematica (TraditionalForm typesetting?)
More powerful text processing Using Mathematica to create slides
There were also others, however, and also before the year 2011. In general you should anyway start from learning the basics, even before you start looking up the archive. Many of the questions you asked here will then disappear by themselves. In particular, it is of a general knowledge that it is strongly advised against the use of capital letters and capitalized words in input cells for custom-defined variables, though you may freely use them in the text cells.