It is up to you which you are selling. Commsec doesn't care. All it needs to know is that you have sufficient units of the stock to sell.
It is really a tax thing and is something you need to decide when you do your tax. Is, for example, the 1000 units you sold those you bought at 2c, 6c or 8c. And you decide that based on which are the more financially or taxably beneficial to you.
I am assuming you are not a trader and are therefore subject to capital gains tax. In that case, perhaps 2 lots of your holding have been held for more than a year and the third for less than a year. Then you might decide for tax that those sold come from the first two lots as they qualify for the 50% discount. Or perhaps all 3 lots are either all held for less than a year or all held for more than a year (so no preference as regards the 50% discount). In this case, you might pick the 2c lots as those sold if you want a bigger capital gain this year or perhaps the 8c if you want to minimise the capital gain this year. This could be important if you have a variable income and you know it is going to be a lot more next year. Then you might want to go for the bigger CG this year when you are perhaps in a lower tax bracket.
You have to keep records of which you decided to nominate as sold and don't be tempted to subsequently alter your records hoping the tax man won't check previous years.
