Keep mortar from the joints when installing the flagstones by removing it during the installation process with a tuckpointing trowel to the level of the bottom of the stone. Wait 36 hours after placing the stone before mortaring the joints.
Mix a batch of mortar in a bucket consisting of one part sand to one part cement with enough water added to create a thick, batter-like consistency. Use an electric drill with paddle bit attachment to mix the grout.
Fill a grout bag with the mixture then close the bag opening.
Place the nozzle of the grout bag against the end of a joint between two flagstones. Lightly squeeze the bag to push the grout out of the nozzle into the joint. Move the nozzle along the length of the joint, filling the space with the grout and overfilling the joint by 1/4 inch. Wait about 10 minutes for the grout to begin to harden and then scrape off the overflow with the edge of the trowel. The grout will scrape off without smearing onto the flagstone surface. If it's too soft to do so then wait another five to 10 minutes before scraping. Wait 36 hours before stepping onto the flagstones after grouting the joints. Allow the mortar to cure completely for about 10 days and then brush the surface of the mortar with concrete sealant to add moisture resistance.