PC3 puts an adjustment on top of whatever is coming out of the ECU. If you are going to use a downloadable map off the internet, then yes, you need to put it back to a stock setting. If you are going to have a map made for your bike on a dyno run, then no. The PC3 would just add to the arrow tune already in your ECU, but only if built off a dyno.
I would suggest going back to stock ECU and then PC3-ing it up. Just to make things more clear in the future plus being able to try other maps and being able to put it back to stock. Of course you are now going to get blasted with a lot of comments on buying a TuneBoy instead

Another fine option.