The Per-Diem rates are defaulted in the table t706v.
Through Transaction PR03 you can claim advances. You cannot claim advances through the Portal.
If you set the Per-Diem rates in the table t706v and create an advance on behalf of an employee then as soon as you save that advance in the transaction, the trip is created in employee's queue. Then the employee has to change that trip and claim his per-Diem.
The logic will automatically deduct the advance amount from the total per-Diem amount and the final amount is created at the output.
In this way he gets advance Per-Diem and when he claims for that trip at that time it will get deducted from advance amount and finally he will get the remaining amount.
Still you have any issue then can you please elaborate your requirement or show me with screen shot so that i get a very clear picture of your requirement.