Can you explain something about the position of the verbs in this sentence?

Hello, I am a beginner in German. There is a sentence in a german text I am reading which goes, "Und da ich weder einen Mechaniker noch Passagiere bei mir hatte, machte ich mich ganz allein an die schwierige Reparatur."

My previous, no doubt flawed, conception of verb position was that they are second position, unless they are infinitive or in perfect, in which case they are last. What makes the position of "hatte" and "machte" different in these sentences. Thank you!