Your question is quite general, and I will try to give some general guidelines.  Odoo can automatic create operations and routes when you have created a warehouse. These will based on best practice operations.  All Best practice is based on that master data is set correctly.  Challenges will happen when flows are not according to preset configuration.  Every internal logistic operation is different from business to business. Even from warehouse to warehouse. But the standard configuration from Odoo will be OK for many. Then also the configuration is quite flexible.

Inbound: Make sure goods receipt is planned to receive in the correct warehouse.  Each warehouse must have it's one receipt operation.  You can control this by two ways: In the purchase order, you can select the warehouse. You can you can also set routes on products or product categories to direct product to the correct warehouse.

Transfer: You set up predefined routes with rules which would basically say: If there is a requirement for a product in one warehouse, then create a transfer to do automatic.  This is also a setting you can do on the warehouse: Set warehouse A is supplied from  warehouse C.  Odoo can then automatic create the routes you need, as well as transfer location.  This will result in: An outbound delivery and picking will be created in the sending warehouse with destination to the transfer location, and a receipt will be created in the receiving warehouse to receive from the transfer location. 

Efficient operation: Label everything with barcodes. Invest in proper handheld terminals with high quality bar code readers. Be paperless.  Papers get lost. So if you base your process on printing out i.ex picking list to tell the operators what to do, experience tells you will be missing something.  

I am not very happy about the barcode app from Odoo. There are others with a lot more flexible possible configuration that can be used.

Be accurate on planning dates and times. So when operators looks up the list of transfers to do, the one of the top, should be the first to process. 

Ad hock transfer. Most businesses will experience that they need to transfer something that is not planned.  Never transfer anything without registration. 

So to sum up: Best practice is a combination of best fit configuration and organize work properly.

I hope this partly answer you question.  But best practice in almost any business operation can easily require a full day seminar.