If you sell the shares purchased at $3.45, you incur a capital gain or loss on those shares only. The other parcels are of no interest to the ATO until you sell them. Make sure to note which shares you have sold at the time of sale though. If audited by the ATO, you need to be able to provide proof that you considered you were selling that parcel and not using the first-in-first-out approach, which is more or less the default.
As for your second question, you pay tax on just the ones you sell. Your calculation of capital gain made should show 5,000 purchased at $1 and sold at $2 with 50% of original brokerage when you bought and 100% of the sale brokerage added to the purchase cost.
