This is a fun project to spruce up a newly planted garden. Plus it's a perfect activity for getting artistic (and maybe a little messy) outside.
When you're picking out the acrylic paint, you just need to look for two things on the label. First, check the front and make sure it's good for exterior/outdoor use. Second, turn it over and check that the instructions say something like "clean up with soap and water". That means the paint is water-based and therefore easy to clean up. I found these little touch-up sized jars at a hardware store, but a hobby shop would be a good bet, too.
We like setting up outdoors to minimize clean-up. Kids should be dressed in "paint clothes" or covered with a really big smock -- an adult's button-down shirt turned around backwards works really well. To clean up, just rinse out the brushes in the pail of water (no need to get an indoor sink dirty). Tip: set brushes to dry with the bristles pointing up -- this prevents the tips from getting stiff. If you're creating garden markers, it really helps to give the child a photo of what the grown plant or vegetable will look like. (The pictures on seed packets are perfect for this.) This is a great way to talk to kids about how plants grow from seeds! When the painting is done, set the rock aside to dry overnight. Then, if you'd like, take a permanent marker and write the name of the plant.