For some setups, trades will flow from the API to the company and be sent to the traders again. A good example of this would be a TT Rest or Rithmic setup. You would setup 1 user id connecting to the API and that user has access to many users' accounts. When the data comes into the company, it will be disseminated to the individual users according to which account was set in Assign Account
When trades are imported, you have the option to use the commissions set at company level or those at trader level. Go to the Company Settings screen and enable the "Use Commissions from Company on Import"
Enabled - uses company level commissions
Disabled - uses commissions from employee account
Note that employees can still override commissions by using the "Apply Commissions" option on their account.