On most flagstone walks that I have installedI prefer to have a rough surface that I can place my mortar on. When mixing the mortar add a product called Abitol, it is an acrilic polymer bonding agent. Mix your mortar with .5" of slump, slop some abitol on the raw concrete and stone, slather mortar on generously and place your flagstone with the aid of a straight edge to maintain grade. After stone is placed, beat the heck out of it with a rubber mallet in order to seat the stone to the mortar base. When you have 5 - 8 joints done, use a wet sponge to seal the mortar in the joints and clean your stones.
At this time of the year, you will want to cover the work overnight with bubble cover in order to maintain a temp above freezing. Do not use the walkway for 48 - 72 hours after completion.
The stones that you have left over will need to be cleaned of the old mortar, and possibly acid washed in order to ensure a good bond when you are laying them.
If you would like the name of a good landscape contractor shoot me a PM and I will be happy to send you one. I no longer do this type of work, getting too old.