Ok so you will have the ms1 ecu. And it will be running ms1Extra software found at the first link I posted.
The msns-extra daughterboard is an extra board thats been fitted to give your ecu extra features such as boost control, launch control, VR input etc.
On the fuel and spark tables you can actually set the RPM and map values to whatever you want. 100kpa is zero boost, below that the manifold is under vacum, above 100kpa is boost. Make sure the numbers on the kpa scale go past 100kpa or you wont be able to tune for boost.
Eg
http://www.msextra.com/manuals/MS_Extra_Tuning_Manual.htm#sparkmap
The other thing is that it may have been setup for Alpha-N (tps vs Rpm instead of map vs rpm).
This link from the manuals may help.
http://www.msextra.com/manuals/MS_Extra_Tuning_Manual.htm#VESetts
Any chance you could post up the .msq?