In APVAT Act, the sale price is defined under Section 2 of the APVAT Act, 2005. According to this defintion t he sale price will included the duties of excise but will not include the amount of any tax charged under APVAT Act read with APVAT Rules, hence, in the Online returns, the taxable amount will be e ntered.
On the basis of this taxable amount the liablity of tax under APVAT will be calculated, which should be reconciled with your financial otherwise, you would have to provide the justification or reconciliation at the time of Assessment /Audits duly conduted by the APVAT Department.
Please check the definition of the Sale Price under APVAT Act, 2005.