In the storefront code I can see that the Shopping cart has a Comment property and also the LineItem has a Comment property. I also found that there is a text area for entering "Special instructions for seller" in the checkout page.
My questions are:
1- Where the "Special instructions for seller" is stored since I could not see it in the order section in admin panel.
2- For the LineItem comment, how can the customer add his comment? or is it for the store manager?
This doesn't implemented yet, but I've added new task related to you question https://github.com/VirtoCommerce/vc-platform/issues/967 and you might track implementation progress there.