Hi folks - this is probably simple but i’m getting myself confused so probably best to ask for help please.
I’m a new user and have two local vaults that i’m trying to use with Obsician Sync so I can have them as two, separate remote vaults.
Should be straightforward, but i’m ending up with either having duplicate vaults created locally or duplicate, nested structures crreated within the vaults.
Help please!
(I know the obvious thing is to only have one vault, but I want to keep these two separate for now at least)
thanks!
Just to rule this out first: Are you on the Standard or Plus Obsidian Sync plan?
The Standard plan only supports syncing one vault.
Plus - although that wolud have been an easy fix! 
Have you followed the steps in the documentation (Set up Obsidian Sync - Obsidian Help) ?
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+1 to Zodian, and carefully going through the docs.
Are you making sure to clearly distinguish between creating a vault (you already have them created) and connecting to a remote vault?
- Set up Sync for the first time: Set up Obsidian Sync - Obsidian Help
- Then sync it on another device by connecting to the remote vault: Set up Obsidian Sync - Obsidian Help
- Make sure you aren’t trying to setup a Sync vault in any 3rd party syncing like iCloud or OneDrive.
- Make sure you make a backup now if you haven’t already, in case the folders keep nesting in weird ways.
- Personal tip: Don’t name your vault “vault” or “obsidian” or anything generic that will make it confusing to know which folder to choose.