BNR stage 1 is an excellent "plug and play" to replace the stock turbo. The flow pattern is so close to stock that you can run it with stock ECU or Hypertech. An aftermarket manifold makes no sense with that turbo as it will not produce meaningful gains.
To benefit from the manifold you will need to go with BNR stage 2 or 3. Either will require a custom tune with AP, and Stage 3 requires a larger turbo inlet pipe too, IIRC.
If you haven't done so already and you want the BNR Stage 1, your compatible exhaust power increasing mods will be replacing the stock downpipe and mid pipe with good 3 inch aftermarket dp/rp. Serious power gains with that. And you can stay with stock tune or get good gains with Hypertech or a well chosen OTS AP tune.