I thought when I filed my 2018 extension I made a payment of $1,200, However the $1,200 payment has not yet been deducted from my checking account.

Was the extension successfully filed ?  And did you have the correct debit info ? 

Use this TurboTax website to check the status of an e-filed extension and if it was either accepted or rejected -https://turbotax.intuit.com/tax-tools/efile-status-lookup/