You can do any manual pause/resume that you like and the plugin will not care. With the scheduled ones there is a specific task kicked of at the scheduled time to attempt the required action. If the action is not appropriate (e.g. pause an already paused check) then that task simply exits taking no action.
Note that you can use the temperature related pause/resume in addition. If this is active then a ‘monitor’ task is run reasonably frequently to see if a temperature related pause/resume is appropriate. That way if you are having temperature related issues you could get pause/resumes happening within the time period for the scheduled pause/resume, or if you have started the check manually at any time.