In a saucepan, add the 6 cups of water and the the kombu. If using shiitake mushrooms, add those too. Allow to soak for a few hours or overnight.
If you are short on time, instead of soaking the kombu for hours, you could heat the water in the saucepan to 60 degC and maintain for 1 hour.
Put the saucepan over a medium heat and bring the water and kombu up put to a simmer.
Just before it starts to boil, remove from the heat.
Add the bonito flakes and steep until they sink to the bottom, 5-10 minutes.
Strain the dashi broth through a very fine sieve or muslin. Set aside the steeped kombu and bonito flakes.
[Optional - to make niban dashi - see comments above] In a clean saucepan, add 4 cups water together with the strained ingredients - the kombu and bonito flakes. Bring to a boil then remove from the heat and add another handful of bonito flakes. Allow to cool then strain. Use as a stock.