I have previously written about khipus here and here. It's unknown at present how many khipus were phonetic (like the Collata khipus discussed in the second link). There are a lot of khipus which cannot be interpreted through the decimal system alone, such as the Collata khipus which have no knots at all. These khipus encode non-numerical information such as epistles, histories, and religious information.

Although the khipus are therefore not "just a ledger", there are a lot of numerical khipus. When it comes to figuring out how someone would know what those numbers meant, recent research indicates that it was the cayte. These are needlework bundles at the beginning of many khipus which were used to indicate the subject matter. For example, the red cayte made of deer hair on this khipu is thought to signify the subject of warfare. Caytes have previously been little-studied but there is some soon-to-be-published research by Sabine Hyland looking at the evidence for caytes as subject markers on khipus in the Inca period and afterwards. You can read a little about caytes in this older article of hers.