So happy for all of you doing this trip! I spent a lovely week in Prague a couple of summer ago, happily exploring on my own. A few things I did that I wanted to suggest:
For those wondering about seeing the Jewish quarter, yes definitely do it. Very moving. You buy tickets at the first sight and then follow a map to several others, with an audio tour you can take with you from place to place.
On the grounds of Prague Castle, do not miss the Lobkowicz Palace. It's easy to miss, because the entrance is just tucked in along a wall, but WOW! Ahead of time, you can download Rick Steve's podcast "An American Nobleman in Prague" to get the history of the family and palace and hear from the current prince, William Lobcowicz, who reclaimed the family inheritance after the fall of Communism. This same man narrates the superb audio tour onsite, in which he not only describes the rooms and artwork, but the process of reclaiming and restoring all of it. Truly a fascinating story and I felt like I much better understood the history of the area after doing this.
Other neat things to do include climbing to the top of the bell tower of St. Nicholas church, where it is still set up for Iron Curtain era spying on the citizens below, and a walk around the Loreto, a small pilgrimage church. Anyone doing this trip with teenage daughters may want to plan an hour or so in the Museum of Decorative Arts, with its floors of prewar fashion.
This is such a beautiful, walkable, enjoyable city. You're going to love it!