The Prodigy has an unorthodox layout and airflow isn't all that great, the DS Cube isn't that great of an aircooling case either in its stock form, you would have to kit both cases with good fans to get decent airflow.
It can be a challenge in terms of the power supply, if the power supply is modular you would have to attach the necessary cables before installing the power supply, unless you have Linus sized hands to attach them afterwards, everything else is a breeze though.
Oh and if you plan on changing CPU coolers that require backplates, you will have to take out the motherboard because there is no way to access the back of it once it's installed.