Identify the area where you want to replace grass with ground cover and flagstones. Insert wooden stakes into the four corners of the patio site and stretch a string around the stakes to outline the area. Use landscape paint to mark the areas where you intend to plant ground cover.
Remove grass and other growth from the patio site and keep digging until the surface is 8 inches deep. Flatten the soil with a hand tamper and place landscape fabric over the soil.
Install wood, metal or stone edging around the border of the patio site. If you're using pre-made edging material, drive 10-inch nail spikes through the edging slots to secure it to the ground.
Shovel about 6 inches of gravel over the landscape fabric and use a 2-by-4 to smooth the gravel and create a slight slope to lead water runoff away from the home. Spread coarse sand over the gravel and smooth it evenly.
Set flagstones beginning at one corner and press them into the sand. Leave consistent spacing on all sides of the stones and use a water level to check that the surface is even.
Pour fine sand over the flagstones and pack the sand between the spaces until the joints are filled.
Remove any weeds and stones from the areas where you want to add ground cover and about 3 inches of compost to enrich the soil with good bacteria.
Use a spreader or spread ground cover seeds by hand to cover the entire planting site. Place a thin layer of straw over the seeds to keep them moist. Water the area according to care instructions included with the seeds.