I've been maintaining a personal knowledge vault in Obsidian for a few years now. These are the principles I've settled on — not a system I planned upfront, but habits that survived contact with reality.
(Quite radical and (still in) experimental): write directly and immediately in your vault. That means if an idea belongs to the Vault, do not dump it down to the interim ephemeral notes. Avoid The cost of delayed action.
Write with the quality as if I am about to show it to someone. Writing in prose potentially (I don’t know for sure) comes with the cost of being too elaborated for efficient reread. This can be mitigated by bolding the keywords.
Make connections relentlessly:
Don't write the words down out of tiredness and fear of loss if they don't make sense. The cost of maintaining them outweighs the risk of losing valuable (which is a doubt in this case) thoughts. Don't turn your Vault into a garbage dump.
Writing in the vault is its own reward. The collection of intermediate artifacts grows over time. Ideas solidify, become tangible — and the fragmented starts forming into a holistic whole.