I use color to show whether the text is said silently, or by just the Cantor, or by the whole congregation aloud.   However, be alert to variations in local custom.

During the Torah-Reading section of the service, color is used to indicate which words are said by the Gabbai, which are said by the honoree, and which by the whole congregation aloud .

Headings and instructions are always in black.

Navy blue indicates text that is said by the mourners.   Since this color may be hard to distinguish from blue or black in many browsers, I include explicit instructions wherever it appears.

I use square brackets [  ] around words that are included by only some congregations.   For example:   R'tsei [ na ] vi-m'nu-cha-tei-nu...

And in a few places I use angle brackets and a bar to indicate alternative paths used in different congregations.   Some congregations recite only the word(s) between < and |, while others recite only the word(s) between | and >.   (No congregation would skip both, nor would any recite both.)   For example:

  Sa-b'ei-nu mi-tu-ve-cha,

< sam-chei-nu   |   v'sa-mach   naf-shei-nu > bi-shu-a-te-cha,...

I use parentheses ( ) to indicate traditional congregational interjections and responses that do not actually appear in the traditional Hebrew text. For example:

( A-mein )  

Because a Siddur contains the Name of God, it is treated with reverence.  Do not carry a Siddur with you into a bathroom.  Do not put it on the floor.  If you drop a Siddur, pick it up immediately.  After dropping it, the tradition is to kiss it as you pick it up.  Close the Siddur before leaving it unattended.  Some people also kiss the Siddur as they finish using it, and take care always put it down with its front cover up.  When a Siddur is worn beyond repair and has outlived its usefulness, it is not thrown away.  It is buried respectfully, like a human corpse.  Your nearest Jewish funeral home will be happy to help you dispose of it properly.