There are two ways you can manage this:
1. Keep track of all of your parcels, and when you sell nominate which parcel you are selling and its associated CGT discount implications. This is what you are describing and is perfectly valid.
2. Treat your holdings as one merged holding - in this case you would have 1,000,000 shares eligible for 50% of the applicable CGT discount. If you sell 50% of them the next day, you would be eligible for 50% of the CGT discount (i.e. 25%), and the remaining shares would also be eligible for 50% CGT (and eventually the full 100% if you keep them all for another full year).
In case 1, the important thing is to keep track of individual parcels.
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