There are a few weays to setup Fullfilled by Amazon - and it depends on the retailers needs and how they best want to support it:
Duplicate items in Merchant platform - recommended:
Generally what has worked best for retailers is that they create a duplicate of the item in their ecommerce platform – and set the stock level to the stock they send to Amazon.  When orders are created in Amazon for the FBA product we then create that order back into the retailers platform, but they don’t dispatch as its FBA.
The advantage of this is that all sales are recorded in the retailers ecommerce platform, so all reporting/gst calculations/etc work how they currently do.   They can easily see how much stock sits in Amazon too
The disadvantage is that you have two products in the system (general you would set the FBA product to invisible).
Single item:
This is the simplest approach and the retailer would simply set items that retailers wants to FBA, and they would update.  Orders can either be sent back to retailer or not sent back.
The advantage is its very easy to do, especially when testing viability of FBA.
The disadvantage is that you might not have accurate record of sales in ecommerce platform, you can only have either FBA or FBM at one time for a product.
FBA account within IR platform:
This is where Intelligent Reach setup a second account for the retailer in the platform, and change all SKU to postfix with FBA and then sync to amazon.
The advantage is that all products can be FBA, and be updated based on merchant data.
The disadvantage is that two accounts are in the system, so need to be setup optimised and managed separately, so extra costs involved.  Orders are not passed back to ecommerce platform so there isn’t an accurate record of sales in ecommerce platform