Based on the below example from the ATO for 'Sarah'
The example as follows. This assumes you will be preparing the BAS manually (not via SBR).
Sarah imports some computers with a cost of $20,000. The GST deferred on this shipment is $2,000
Entered a payment for 20,000 with a GST code so that its included at G11, and GST total of 0.00
She makes other business purchases in Australia of $16,500, which includes a total of $1,500 GST
Entered payment for 15,000 + 1500 GST
Sarah makes $33,000 worth of computer sales to retailers during June. This includes $3,000 of GST collected (these computers are a combination of existing and new stock).
Entered payment for 30000 + 3000 GST
Sarah’s total purchases (Label G11) are the total of her Australian purchases and the importation, including GST ($16,500 + $22,000).
To increase the amount reported at G11 by 2000 we enter the below journal
(To set up the journal account: use Trading expense account.)
This is the resulting BAS, which has the is correct net amount. The prepopulated field 7A is not included in this form, so you would need to manually increase (by using the journal entry) the amount being reported at 1B with the amount that ATO have prepopulated in 7A.