If I understand you correctly you are describing the following scenario.
Check one item, then click Add tag, for tag write 'Work'
Then check the same item again, Add tag and again write 'Work'

This will create the same tag twice over the same time period.

On the main window you have four timelines and these timelines are all independent of one another. When you check something you are essentially just selecting time.

So lets say I select all firefox usages, I just selected time. Even though I checked all firefox usages, MT wont do anything with them. All you did was select time.

When we first released the software it was without checkboxes, the only way you could tag time was just by dragging on the timelines. We later added checkboxes so that you could assign time more accurately if you wanted, but what you do by dragging and what you do with checkboxes is the same, you are just selecting time.

You could for example drag to select time between midnight and 6am and tag it as sleeping, even though computer wasn't even running.

To edit or delete tags either right click on them on the tag timeline or click on the tag timeline to select it. Once you select it, the bottom part will display individual tags and you can then right click them to again either delete or edit.

Hope this helps.