I am setting up Group RRSP with the company matching the employee contribution. How can I track the employer portion using additional payroll user-defined expense account when some employees are fixed amount each pay and others are % of gross earnings.

Hello Grant,

I just answered a very similar question in this thread so check it out! 

The only difference with your question is the part about calculating the % of gross for some employees and others paying a fixed amount.  User-defined expenses in Simply Accounting are set as fixed amounts.  For the employees who you contribute to based on a percentage, you would need to manually calculate the figure and adjust the user-defined expense portion on the paycheque each pay day.  The figures in the User-defined expense tab can be modified on the cheque.