It depends on what you are attempting to do. But if you look at the Access tab of the AClient properties, you can pick and choose what the user gets prompted for. I am assuming that you would want to uncheck the "Copy file and Run command" checkbox under the "Prompt the user before performing actions". These settings can be done remotely from the console and for groups at a time. Just right-click on the computer (or folder, or all computers), click Change Agent Settings, Production Agent and then click on the Access tab and make the appropriate changes. When you click OK, the machines that are online will be updated at the AClient will reset itself (no prompt that the end user will see for this).
Hope this helps.