(usually you're suppose to wash the jeans before you even wear them... so yah) wash your jeans in cold water and vinegar. if you want to keep the shape, handwash them NEVAH EVAH put them in the dryer and hang them. keep doing it 3 timesand maybe even leave them in the cold water and vinegar over night.
Indigo is a dye so if it bleeds onto your kicks there is little chance you're gonna be able to clean it up especially if it's a porous material like suede...if it's on hard leather try jason mark or even some regular rubbing alcohol (be careful with painted midsole areas with the alcohol)
...the best preventative thing you can do is use some clear scotch tape or masking tape and tape the underside of your cuff. If you don't rock a cuff it is a lil harder because the exterior of indigo denim holds much more dye then the slub.