Primary stress primary stress is marked by a macron (horizontal line) below the vowel of the stressed syllable.
Vowels reduced to mid central (marked in IPA as schwa ə), plentiful in English, are normally marked by a dot below, but when stressed, a vertical line below is used instead: otherwise otherwise. Depending on the dialect and particular word, these vowels may be realized differently, as /ʌ/ or even /ɜ/. However, in General American accent, no such distinction is present, so it is not (for now) honored within English Phonemic Spelling.
Silent letters are marked with an inverted breve (sad face curve) below or above: subtle, honest, though. As you can see, the only exception is the letter e, which is always silent on its own, and is only voiced when marked with an accent.
Consecutive letters of equal phonetic value are pronounced as if there was only one. That's why multiple vowel letters representing only one vowel sound all get diacritics, e.g. said, cough