Learn Polish: Pracujesz w poniedziałek czy we wtorek? - Do you work on Monday or on Tuesday?

Both w and we mean "on" here. We change w to we before words that start with certain difficult consonant combinations (like wt- in wtorek) to make pronunciation easier. Saying "w wtorek" would be quite a tongue twister!

The lesson says to use the Accusative case for days of the week after w. Why haven't poniedziałek and wtorek changed their endings?

They actually are in the Accusative case! In Polish, for non-living masculine nouns (which includes most days of the week), the Accusative form looks exactly the same as the basic dictionary form. So, the words do not change their shape here.

Doesn't czy usually start a yes/no question? Why is it in the middle of this sentence?

Yes, at the start of a sentence, czy is a question word used for yes/no questions. However, when placed between two options inside a question, czy simply means "or". Here, you are asking the listener to choose between Monday or Tuesday.

Why isn't the word ty (you) used before pracujesz?

In Polish, you can usually drop the subject pronoun because the verb ending tells you exactly who is doing the action. The -sz ending on pracujesz already means "you work", so adding ty isn't necessary unless you want to add special emphasis.