We've need to change our warning text, if i change the message and apply it, do i need to do anything else, or will the client's pick this change up the next time they run a sync?
You set this at the group level correct? Do you have Controlled groups or Uncontrolled Groups? Did you right click the machine or machines and choose 'Reset to group configuration'? If you want to change for the whole group, right click the machine group itself and choose 'Reset all to Group Configuration'. Sync the machine(s) and this should update the warning text.
Be careful when choosing the option to (or not to) Exclude Users and File Groups. The wrong choice could render your users unable to authenticate to the laptop (among other problems).