Dig a shallow hole for each rock so that it appears to naturally "grow" out of the ground. You may also want to mound some rocks together with soil between them.
Decide where you would like to put the plant material, being mindful of creating rhythm across the breadth of the area by repeating a plant type several times. Place some plants next to the rocks and some in between. It is important to appear random in the spacing to keep a natural look. If your plants are in pots, place the pots in the arrangement you have chosen and check the spacing to make sure you like it. Keep in mind that the plants will grow.
Dig holes twice as wide and a few inches deeper than your plants. Mix in the soil amendments with the soil you dug.
Plant the plants. Keep the soil level the same as it was growing in the pot. Backfill the hole around the plant. Tamp lightly.
Place some low creeping plants in the dirt between the rock mounds. These will add visual appeal and appear to anchor the rocks to the garden.
Water well. Continue to water frequently until plants are established.