Currently an employee, working from home, tags all their time in ManicTime. But its currently an all or nothing approach when it comes to syncing to the server.

Instead .. have an indicator bar on the top of the timelines that shows which segments are to be sync'd to the Server ... an employee selects time on any timeline .. right-clicks and chooses "Submit to Server" .. then that time segment is sync'd to the server based on the server settings of 'what to sync" (E.g. sync everything or specific timelines)

This allows employees to keep track of their time and put things like "Personal, Bathroom Breaks" without it being uploaded to the company server.. It will also avoid ManicTime use in a company from being considered "Surveilance" .. employees will be more apt to use it for their own benefit because they don't have to worry about sharing with their employer.