Spelling is the written form of a word while sound is a spoken component to a word. This is also an important distinction since the sound and spelling of a word might not necessarily match up. (The word enough, for example). You can't rely on the sounds to put down the correct spelling. A main difference in the phonetic inventory of English and Portuguese is the heavy use of the nasals and something called flaps/trills.
There are many sounds in Portuguese that don't exist in English. For example, they have many nasal vowels which we don't have. But they also have different pronounciations for things like "ch" in Portuguese is pronounced like English "sh". As for examples of the nasal vowels, words like pão and mãe are nasalized, and are represented by the ~ on the top of the vowel.
Regarding the sound system, it'll just be a matter of practice and getting these new sounds down. A good way to understand these sounds is to listen to native speakers, through radio, tv, and music. I think it makes the most sense to completely immerse myself to understand the sounds of Portuguese!
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