This
thread tells you all you need to know about when to use SER and ESTAR. Because this question comes up so often, you'll find this post pinned to the top of the grammar forum (it'll always be on top).
The three classes of verbs are just that - three different types of verbs. Each type of verb has its own conjugation rules. Many chapters can be written about verb conjugation, so do yourself a favor - take everything one bite at a time! Eventually, it'll all make sense.
Most people choose HABLAR, COMER and VIVIR as a model for each verb type. They then learn how to conjugate each type into the present tense (the -AR ending is stripped off and a person-appropriate ending is added; the -ER ending is stripped off and a person-appropriate ending is added; the -IR ending is stripped off and a person-appropriate ending is added). Then they tackle another tense. And on it goes.
SER and ESTAR are irregular verbs, as far as conjugation goes, but are still classified by their ending (-ER and -AR). Adding another irregular verb to the list, IR, you've now got a model from each verb class (-AR, -ER- and -IR). Because these verbs are irregular, they deviate from the simpler rules the regular verbs 'enjoy'. I suggest you start with the regular verbs I listed above first. Tackle the irregular verbs only after you've got a handle on the regular verbs.