If we ignore the other merchants that sell via your platform and focus on your company's stocked products:
From your first point: What documents are you creating in D365? You say "orders placed in the web will come to Dynamics then we can follow standard pick, ship process to reduce the stock", which to me, implies you're creating a sales order that creates your revenue, tax, cost of sales, inventory reduction and AR - this would post to the appropriate GL and subledgers. In this case, you'd want to create a payment journal to reduce the AR and receive the payment.
However, based on point 2, I don't think if this is the process you're actually using, so I'm not entirely sure how you're capturing the inventory portion of the transaction.
ASSUMING that you're accounting for the inventory transactions properly through another means, you could create a general journal that records revenue (CR), sales tax (CR) and payment (DR).
With that said - this approach is not best practice. I would be very concerned about traceability of your inventory transactions.
For the case of the transactions being generated for an external merchant: again, not entirely sure you just want to record this directly to revenue and bank - I would assume you'd need to pay your merchant (less a platform commission, perhaps?).
