Como você sabe isso? - It sounds like you are asking about some unexpected knowledge the person showed, or if you find out someone has a really unexpected skill. (In case it is a skill, it would be more common to ask "Como você sabe fazer isso? - How do you know how to do that") Como você sabe disso? - This one sounds like you are asking about a fact the person learned, like a rumor or a piece of gossip.
They can be used interchangeable though, and the second one is way more common.
It's explained on the page I linked. Before vowels 'a', 'o' and 'u', the letter 'c' has to be pronounced /k/, so the 'ç' (called cedilla) is used in these cases to change the pronunciation to /ss/.
So basically when you hear the /ss/ sound, the next letter decides which one it's gonna be: - 'c' before 'i' and 'e' - 'ç' before 'a', 'o' and 'u'
I think of the English equivalent as "How do you know of this?" or "How do you know about this?" - like an old or overly formal way of saying it (fantasy language!). Of course almost no other language has the meaningless "do" so perhaps "How you know of this" or "How you know about this" is another way to think about it.