Yeah i agree with Simon ^^ about Haltech being my choice too.
If all go's well with my car, i'll most likely be installing a haltech ECU, because again if it all go's well (and i dont think how much money i spent so far and need to spend) i'll be running a single turbo, custom intake manifold and most piping and other stuff and will need a aftermarket ECU.
In your case I'd definately use the Haltech to get the most from your setup.
As Jet said, there is a patch/plug in you can use.i can confirm this as it's what I plan to use with my hi-flow motor. Plus it'll be E85/98 tuned as well.
The std ecu is very good in most applications as Steve said.
To give an example of the benefit of a stand alone, my mechanic recently fitted a Haltech to an SR20 in a very reliable track car. Previously ran a PowerFC with 19psi made 317rwhp. With the Haltech on wg only (15psi) made 307. He potential for much more is there as you can see. 10hp for 4psi less is magic. As a general run you are running into diminishing returns when it gets to 10hp per psi.
Again I'm not saying do it, that's for you to decide.