Think you maybe getting confused with the SC pump & the water pump. There is an option to turn the pump on via VCDS and you should hear/feel water passing through the pipework. Sorry I cannot help further as mine is divorced and on a separate loop.
TB upgrade is not essential until you have the charger ported to allow for the extra air flow, spend the money on the remap before going any further. But not APR as they have stop supporting the 3.0tfsi
Sorry mate I am in Kent. There is a VCDS forum which should be help you out.. Its pretty easy to get started. Once installed you then need to test the lead and connect to the car, once that's done then you are good to scan car etc.