Phonology studies sounds and their importance to language. The basic unit of phonology is the phoneme. A phoneme is more than a phonetic distinction, in fact, it often includes multiple phonetic categories lumped into one. For example, a number of different sounds are lumped in with ‘t’. There are rules as to when each type of ‘t’ sound gets used
t-aspirated: [t’] – tired, truck
t-unreleased: [.t] – cotton, button, satin, Latin
t-flap: [ɾ] – better, butter, atom
t-neutral: [t] – center, rapt, sect
Now of course, Phonology is not as clear-cut as this. This is an approximate set of the pronunciations of ‘general American English’, but I find myself differing in a few cases. For example, I pronounce the t in Latin as t-neutral. Some people will pronounce ‘center’ with a t-unreleased.
[t’], [.t], [ɾ] and [t] are all different allophones of the phoneme /t/. Allophones are created by variations in pronunciation that do not affect meaning. If you pronounce butter [bʌtər] or [bʌɾər] (the former having a more pronounced t), your utterance means the same thing. On the other hand [bʌfər] or [bʌbər] indicates a phonemic change, rather than an allophone distinction, and your utterance means something different (buffer) [bʌfər], or nothing at all, in the case of bubber [bʌbər].