Thank you friends 
I have now understood that part of it. I guess I got confused cause I saw all the amounts lying in the Employee Clearing Account and did not see the relevant numbers under the Salary and Transport allowance head.
After your help and having cleared the employee clearing account, I noticed that the amounts still did not reflect in my expense account and that is when I noticed all those amounts lying in my Suspense Account.
When I defined the payslip items, I had selected Salary and chose the salary account and for transport allowance I chose the Transport Allowance account. Would you know why it still debits those to the suspense account?
Thanks again for all the help