If you have been fully using Independence for the whole of the tax year, it will have sufficient data to calculate your IR35 liability. It automatically extracts the data and then does the calculation.

You are given the chance to enter the items which are not otherwise recorded: Pension Contributions, Benefits in Kind and, less commonly, Capital Allowances and benefits received elsewhere. The same report that is used throughout the year to show each employee's liability is then used to calculate the final figures (you can see an example here). If you accept them (reluctantly) they can be added to the payroll as a Month 13 payment so that they will be automatically included in the totals on forms P14, P60, P35, P11 etc.

Revenue received during the year for contracts caught by IR35;
Allowable expenses paid for during the year;
Details of pay, tax and NICs already paid;

The amounts in the red box at the bottom are the extra 'deemed' payment in month 13.