how you mount the thing shouldn't matter, as long as it is full of water and does not have an air pocket in it anywhere - maybe that is what one of the 3 water pipes is for (bleeding?)

Austen is correct about the water direction though. think about it like this - the air coming into the chargecooler from the compressor is hottest, so the hottest water will still be capable of cooling it. the air leaving the chargecooler will already have been cooled down, so you need to use the freshly cooled water from the radiator to be able to cool to further.