You shouldn’t be doing Journals with regards to GST activity.
On the Customs Invoice where you were charged the importation GST, you need to input it over two lines.
The first line includes the Purchase Invoice value so the GST is calculated out = 1000 + 100
The second line includes the Purchase Invoice value as a negative and no GST = -1000 + 0
Now the Purchase Invoices cancel themselves out so the Customs Invoice total remains unchanged and the GST component of the that invoice is taken up.
You can read the whole importing process in this topic
However if you are in Australia, there is a specific GST Import Tax Code which can be used