Personal Tax Allowance and Student Loan

So I've been trying to sort out my self assessments as it's the first year I've needed to do this so quite a learning curve! My tax code is 1263L as I get some extra allowance through work. However, I'm not sure where I need to put this into my returns online as I couldn't spot anything obvious. Additionally, with my income I have my basic pay, bonus pay, taxable benefits and then some shares which are purchase before taxed. So my P60 from my employer shows basic pay + bonus pay + taxable benefits - shares. However, I've spoken to HR and they have said that my student loan calculation is assessed on basic + bonus - shares and completely ignores the taxable benefits. I'm not sure on how to evidence this, or if payslips should just do? Additionally, I don't know how to get my self-assessments to reflect this as it's showing that I've not paid enough student loan just on my employed income. Can anyone offer guidance on the above?

Hi,

On your employment page online it asks if you want to claim expenses while working for the employment. If you answer yes to this question it will open the expenses section were you can claim the expenses that increased your tax code to 1263L. If you received taxable benefits that were not taxed through your payroll then you should have received a form P11d that gives a breakdown of the taxable benefits. On the employment page you would answer yes to the question Have you received any taxable benefits and expenses payments. This will open the benefits section to declare the taxable benefit information from your P11d. 

Thank you.