Once you connect your Amazon account to Inventory Planner, you will see separate FBA warehouses for each country in that Amazon region and an FBM warehouse. Therefore, you only need to connect one Amazon account per region to Inventory Planner. 

For example here, with one Amazon US account connected, we see FBA CA, FBA US, FBA MX, and FBM NA created as a result automatically in Inventory Planner.

In Connections & Warehouse settings (Account > Settings), disable any warehouses where you do not need to see detail.

Here only FBA US is enabled.

Shipments synced from your Seller Central account to Inventory Planner can show as either purchase orders or transfers in the Purchase Order & Transfer section of your account. For transfers, a default 'source warehouse' can be configured. To change default settings for inbound shipments, click the gear icon for the corresponding warehouse.

Scroll down to see the 'Inbound Shipment Order Type' dropdown field.

Select from either Purchase Order or Transfers.

If you're configuring shipments to show as transfers, then select a 'source warehouse' for the transfer.

Finally, click Save Changes.
Future shipments will show this configuration in the 'From' column on the Purchase Orders & Transfers page.

Prep warehouses and other warehouses used for receiving, prep, and bundling can be set up as an IP warehouse.

An IP warehouse is used when your store has inventory in a location that does not fulfill customer orders directly. This manual warehouse is used to transfer stock to other locations that do handle order fulfillment. 

In Inventory Planner, IP warehouse stock is imported when the warehouse is created. Then stock is added through receiving a purchase order or warehouse transfer. Stock is depleted by creating a transfer to another location. Finally, stock can be manually updated within Inventory Planner if a correction is needed.

Read more here about setting up an IP warehouse.

If you need to see demand, replenishment recommendations, and reporting for more than one warehouse, then a combined warehouse will show you this information.

Click here to learn about setting up a combined warehouse.

Once this is set up, you can use the combined warehouse for replenishment recommendation while receive to a physical warehouse (whereas the combined warehouse is a virtual warehouse).