The tax code does not affect the amount of Personal Allowance available, only how it is collected under PAYE.

For Self Assessment purposes the PAYE actually paid should be entered on the Employment screen based on the figures given in the P60. This P60 figure will have already taken into account the PAYE coding so no further adjustment is required for the Self Assessment tax return. 

The computation will have the same personal allowance for all taxpayers unless they are born after 1938, have income of over £100,000 or do not have the Personal Allowance due to Residency status. 

If there is underpaid tax for the previous tax year that has not been entered in then this can be entered on the Underpayments, overpayments and adjustments screen, similarly employee benefits can be entered in through the Employment screen.