Here's how I got all of the system flushed on my 996:
Hook the pic flush tool up to the thermostat hose. This will backflush the system. Use the garden hose for this, then plumb in a funnel and run a couple of gallons of distilled water through. You'll be in good shape.
Be careful about how much pressure you use...the 996/986 system only goes to about 20 psi, which is pretty low.