When you install the Kaseya agent on any Windows machine you end up with the Kaseya icon in the Windows start menu. To be honest, the icon in the "Start Menu, All Programs" folder is quite useless for the end user. The agent icon down in the system tray on the other hand is awesome! Not to confues anybody with that. You can remove the Kaseya folder all together with a Kaseya Agent Procedure after install, but even better:
You can remove the Kaseya Agent folder in the Windows start menu during the installation of the Kaseya agent. To do this, edit or create a new customized agent.
In step 3 you can add custom install switches. If you add the /J switch, the Kaseya agent installation will not be added in the start-menu.
Give it a try.