You are using the wrong page most likely. I had these issues in the past when booking hotel or car only for part of the trip. Don't use the page called "Flight and Hotel" or "Flight and car". You must use the custom booking page which is not that easy to find (I bookmarked it). The hotel or car needs to be for minimum 3 days I believe for deposit to work.
I now almost exclusively book flights with a car or hotel for part of the trip so I am very familiar with your issue