1
According to the Oxford English Dictionary, the first meaning of tone is the musical quality of sound:
I.1.a. A musical or vocal sound considered with reference to its quality, as acute or grave, sweet or harsh, loud or soft, clear or dull.
When referring to spoken language, tone means the emotional quality of speech:
I.5.a. A particular quality, pitch, modulation, or inflection of the voice expressing or indicating affirmation, interrogation, hesitation, decision, or some feeling or emotion; vocal expression.
Transferred to writing, tone means the indirect expression of emotion through the style of writing:
I.5.d. transferred. A particular style in discourse or writing, which expresses the person's sentiment or reveals his or her character; also spec. in literary criticism, an author's attitude to his or her subject matter or audience; the distinctive mood created by this.
Tone is also a synonym to mood:
II.8. A state or temper of mind; mood, disposition.
The surviving primary meaning of mood is the temporary emotional state of mind of a person:
3.a. A prevailing but temporary state of mind or feeling; a person's humour, temper, or disposition at a particular time (later also applied to a crowd of people or other collective body).
Transferred to writing, mood refers to the main emotion that a piece of writing evokes thoughout its whole length:
3.c. The pervading atmosphere or tone of a particular place, event, or period; that quality of a work of art or literature which evokes or recalls a certain emotion or state of mind.
In short, when referring to a piece of writing, tone refers to the quality of the narrator's voice: how he or she says what they say. The tone may change from part to part. Mood is the emotional effect that the whole piece has on the reader, not only through the tone of the narrator but also through the content of the narrative and all other aspects of the work.
2
Every writing has tone and mood, including traffic signs and this answer. The tone of a traffic sign is usually sober and informative and the mood it evokes in the interested reader of a traffic sign is usually one of calm control.
Tone is manipulative in that it is employed to evoke a certain emotion in the reader. Whether being manipulative of the emotions of your readers is moral or not will depend on the circumstances. In my opinion, for example, manipulating the emotions of the listeners of a political speech is immoral – because we don't want emotions to guide voters, but arguments and deliberation.
On the other hand, every writing has a tone. The expression of emotion is one of the main purposes of communication and cannot be avoided because we always have emotions and always communicate them. It is therefore almost impossible to avoid affecting the emotions of your readers (or listeners).
The moral writer of non-fiction, therefore, will write the truth and choose a tone that is in accordance with the message. For example, if you congratulate someone to their birthday, the tone of your writing may be joyful, while if you express your condolences because a relative of the reader has died, a sad tone is befitting. This is not manipulative, nor morally wrong, if the emotion you express is one that you acutally have.
3
Tone and mood are dependent on voice. This becomes most apparent in spoken language. A man with a deep and quiet voice will have a soothing effect on his listeners (which is why the voices of tv and radio speakers are technically manipulated to have stronger bass notes), the voice of a child will put most adults in a friendly mood, and so on.
There is no tonal quality to the voice of the narrator of a written text, and in this context "voice" is used to encompass the narrator's viewpoint (that is, their opinion), their tone (that is, how to they say what they say) and so on, that is, how they express their personality through their words.
The tone of the narrator is partly an effect of their voice (the personality behind and expressed through their voice) and partly something the narrator employs intentionally – in the same way that you can change the tone of your voice intentionally.
How much you can do so will depend on your vocal training and the control you have over your emotions: professional speakers such as actors can "lie" with their tone, that is, they can express an emotion they do not have, while the average person may not be able to hide their true feelings completely. The same goes for writing: an experienced writer will have more control over the voice of their narrator and be able to employ it according to their intent, while the beginning writer will most often write in their own tone of voice.
4
Mastery of any aspect of writing, in my opinion, is mostly unconscious. In this, writing is like speaking. When you speak your mother tongue, you don't construct the sentences you speak from your knowledge of grammatial rules and the meanings that the words have. Most native speakers of a language don't understand it's grammar and cannot well explain the meaning of most words they use. And yet we have all learned our mother tongues by understanding its grammar and the meaning of its words. But unlike learners of a foreign language, we have not learned the grammar of our native language through grammatical terms and by memorizing lists of words and their meanings, but by observing language use and trying to emulate what we observed.
Learning writing, in my opinion, works the same. You do not read how-to-write books or scholarly analyses of literature and apply the rules that they list. Instead you read and your write until what you write flows and feels natural and has the effect on your readers that you want.
Writing from rules will result in writing that is stiff and unnatural.
