Company sharesave and company pension

On payroll should sharesave and pension payments be deducted from employees salaries before or after applying PAYE? We have conflicting answers from various pension providers. Pension is calculated as a percentage of taxable income, but if you have two employees on the same gross salary and only one has joined the sharesave scheme his pension and of course the company's contribution will be less than the employee who has not joined the sharesave scheme. This cannot be correct, but how else can it be dealt with so that both employees would receive tax relief and the company would contribute the same amount into the pension.

Would appreciate any comments, please.

Thanks Pete Bird.
Peter Bird