Learn Turkish: Genellikle saat kaçta uyanıyorsun? - At what time do you usually wake up?

Saat kaç simply asks "What time is it?" (literally "hour how many"). By adding the location ending -ta (meaning "at"), it becomes saat kaçta ("at what time"). We use this because we want to know at what time the action happens, not just what the clock says right now.

Why does the verb use the present continuous ending -ıyor if this is a general habit?

In English, we use the simple present tense for habits ("do you wake up"). In Turkish, it is very common to use the present continuous tense (-ıyor) for both things happening right now AND for everyday habits and routines.

How do the pieces in uyanıyorsun fit together?

The base verb is uyanmak (to wake up). We drop -mak to get the root uyan-. Then we add the present continuous tense marker -ıyor and the "you" ending -sun. So, uyan-ıyor-sun means "you wake up" or "you are waking up".

Can I change the word order and put genellikle in the middle?

It's best to keep saat kaçta right next to the verb. In Turkish, the specific question word you want answered usually goes immediately before the verb. Genellikle (usually) just sets the background context, so it belongs at the start of the sentence.