Install it first. Once you install the turbo, you will only have to make slight modifications to your table due to a SLIGHT decrease in VE (the turbo restricts intake/exhaust while it's not boosting), but will run relatively good still. The megasquirt will just start picking up boost and know what to do with it, no reason to wait, and I recommend getting all the kinks with the megasquirt worked out BEFORE your boosted and able to really kill the motor fast ;).