Your question is a little ambiguous, but I'll have a go at explaining a couple of different scenarios as best I understand it. I'll do this based on the current 15% tax rules, because I don't understand how capital gains discounts will work with the proposed new structure.
I've also described how (I understand) it works for an SMSF. A lot of the intermediate calculations are taken care of by your super fund if you are with an industry fund or a for-profit fund and you just get told the end number.
Accumulation Account Only
Let's say there's $10m of VAS in a SMSF and I am the only member of that SMSF (I wish!). My SMSF bought 100,000 units of VAS five years ago when they were $50. They are now $100.
VAS has a distribution of $10 per unit (10%) for the year. Let's assume that the $10 is income from dividends - in reality, it may have some capital gains and other things mixed in, but that complicates the tax picture. But let's say there is a further $2 per unit of franking credits attaching.
The SMSF will receive $1m in distributions from Vanguard, plus $200k in franking credits. The tax payable on the income is $180,000 (currently 15% of $1.2m). But the SMSF has $200k in franking credits. Therefore, the SMSF will receive a $20k refund from the ATO.
If at the end of the year, VAS's price goes from $100 to $110 but the SMSF doesn't sell any units, the SMSF has made an unrealised capital gain of $1m. No tax is paid on this because the gain is not realised.
Without withdrawals, the balance of the SMSF is $12.02m at year end. $10m original balance, plus $1m distributions, plus $20k tax refund plus $1m unrealised capital gain from the year.
So the net tax payable for the year in this scenario is actually a $20k refund.
Where it potentially gets confusing is that MY superannuation balance is not $12.02m in this case. If the SMSF liquidates all its assets, then there is a capital gains tax liability generated. The capital gain would be $6m (since there are 100,000 units of VAS bought at $50 and sold at $110). Because they have been held for more than 12 months, they receive a discount to the capital gains tax. Inside super, capital gains on assets held for more than 12 months are taxed at 10% (less than 12 months it's 15%). So there's an unrealised capital gains tax liability of $600k.
So out of the SMSF value of $12.02m, $11.42m would be 'my super balance' and $600k would be 'reserved' as a tax liability.
In comparison, at the start of the year, my balance would have been $9.5m and $500k would have been 'reserved' as a tax liability.
Pension Account and Accumulation Account
Let's say I'm now past the preservation age. I can transfer some of my accumulation account into a pension account. But no more than $1.7m (this is indexed - it started at $1.6m a couple of years back, will most likely be $1.8m by 1 July this year).
Let's say I put $1.7m a couple of years ago and that has now grown to $2m. That whole amount is completely tax free. No tax is paid on dividends or distributions, I'd receive franking credits as a cash back, no tax is payable on any realised capital gains on this amount. The catch is that I'd have to withdraw a minimum amount from my pension account each year, increasing as I age.
The rest stays in the accumulation account and is treated as above.
If I'm over 60, I can generally also withdraw from my accumulation account tax free. However, I may have to sell down some assets to facilitate the withdrawal. Whilst the withdrawal itself is tax free, if I realise a capital gain on selling those assets, then capital gains tax will be payable.
