After entering commission rates, you might want to apply them to existing positions. To do that use the "Apply Commissions" page on the Tools menu.
If you are logged on as an individual trader, you will see the following page:
At this point, you can select an account or let it apply commissions to all accounts.
When you click "Apply", it will find all the fills in the selected date range, apply the relevant commissions to those fills and then recalculate the total commissions for the positions for the fills.
If you are logged on as a company administrator, you will see the following page:
No account can be selected as the apply commissions will be applied to all trades for traders that are registered to your company. Clicking Apply will override the commissions for their fills and positions for the date range.