There are a few different ways that you can clean suede shoes including the following:
1. Make sure that the shoes are completely dry. Using a brush designed for use on suede, start brushing away the dirt. Focus on brushing in one direction rather than scrubbing back and forth. 
2. For scuff marks, try rubbing a pencil eraser back and forth on the mark until it disappears. Test a small area before doing the entire scuff mark to make sure the eraser won't leave additional marks on the suede.  If an eraser isn't powerful enough, you can also try an emery board.
3. To re-fluff the suede up after you clean it or to give new life to areas that have worn down over time, you can firmly brush the surface of the suede with a stiff brush to raise the nap back up again.
4. To remove water stains, spray the outside of the shoes lightly with water. Use a brush to gently rub away the edges of the water stains. Blot up any excess water with a towel so that the shoes will dry evenly, helping to prevent further water stains from forming. Insert a shoe form or shoe tree in each of the shoes to help them hold their shape as they dry. After the shoes are dry, brush them out with a suede brush to fluff up the surface of the suede again. 
5. Try using rubbing alcohol to remove ink stains. Hairspray also works. However, you may want to test it on an inconspicuous spot such as the tongue of the shoe underneath the laces to make sure that it won't leave additional marks on the shoes.
Here are some more ideas you can try for stubborn stains: