You should report the payment as an additional extension payment to the CA FTB reported in line 39 of form 540. Since you made the payment in 2006 it is not deductible for 2005 tax purposes. You report your use tax liability on line 51 of Form 540.
If you have overpaid tax on line 49 of Form 540, then you will subtract line 51 and 68 from line 49 in arriving at the amount refundable on line 69 or payable on line 70. If you have an amount payable on line 50 then you will add the use tax liability on line 51 to arrive at the amount due on line 70.
Because it is impossible for me to identify and consider ALL the relevant facts, this advice is not intended or written to be used for the purpose of avoiding penalties, and cannot be used for that purpose.