Ah, in that case you could add some code like this:
{% if product.variants.first.inventory_quantity < 100 %}<p>Please note this product is currently on backorder</p>
{% endif %}Orders will come through as per normal. All the sync task is doing in Shopify Assistant is looking at the line items were ordered and if it sees a variant that has been configured it reduces the inventory quantity by the the quantity ordered (and adds it back if the order is cancelled).
E.g. If you have Var 1 - $3, Var 2 - $4. You have set up Var 2 to sync inventory of Var 1 when an order comes in. Customer creates an order containing 1 x Var 2. In the background, Shopify Assistant sees the order and will now reduce inventory of Var 1 by 1.
It is free to try it out so please feel free to give it a trial to see if it meets your needs.
Thanks, Gavin.