If you use manufactured stone it will come in standard height and you can put it on top of the concrete. Just ask the people who would install it, since they already gave you a quote for installation.

If you use natural flagstone, it will come in irregular heights and you will need to level it with sand or mortar. If sand, you need a perimeter wall to hold the sand in, and then will have to worry about drainage and your stones floating in sand soup with a heavy rain. Mortar would solve that, unless you live in an area with frost heave, then you have a bunch of other problems.

Why did your concrete patio crack?

Search this forum, this has been asked before.

if your page is cracked i would tend to lean agaist removing it, chances are there are underlying reasons why it has cracked, remove the pad, and lay 6 inches compacted 2a, and then 1-2 inches sand the the product whatecer you chose