You can use Tag editor for all sorts of tag operations - rename, change color, delete, change ordering...
To open Tag editor, click on down arrow on the left side of Tag timeline and choose Tag editor.

There are four tabs:

• Tag combinations
• Tags
• Inconsistent tag order
• Tag shortcuts
• Tag sources

Tag combinations

In ManicTime, tags are separated with comma, for example:

• Project 1, Testing
• Project 1, Design
• Project 2, Design
• Project 2, Testing

In above example tag combinations are:

• Project 1, Testing
• Project 1, Design
• Project 2, Design
• Project 2, Testing

 while tags are

• Project 1
• Project 2
• Design
• Testing

To illustrate the difference between renaming tag combinations and tags lets consider this.
Lets say we want to rename Project 1 to Project Alpha. Since Project 1 is used in two tag combinations, it is best if we rename it on Tags tab. So just renaming Project 1 to Project Alpha all tag combinations which use Project 1, will be renamed to Project Alpha:

• Project Alpha, Testing
• Project Alpha, Design

But if we want to change 'Project Alpha, Testing' to 'Project Alpha, UI testing' and leave 'Project 2, Testing' intact, we need to rename it on Tag combinations tab. 

Multi rename with replace

With Replace you can rename multiple tag combinations at once. To do this:
Select tag combinations (hold down Shift or Ctrl and click items to select more than one)
Click Replace
In Find type the text you want to replace, in Replace with text you want to replace it with.

In the list below you will see what it will look like after you press Ok.

Inconsistent tag order

First a few words on why tag order is important. Up until v2 it was not very important how you tagged. Statistics doesn’t rely on tag order, since you can only see individual tags. When we added Timesheet, tag order became more important. 

For example lets say we tag some time with 'Project 1, Design' and some more with 'Design, Project 1' 

This is the timesheet we get.

Because 'Project 1, Design' and 'Design, Project 1' have the same meaning to me, it would be great if they were one tag instead of two. Inconsistent tag order will show this and you can rename it there. There are two rename buttons, click on the one which is on the side you want to rename.

After we rename 'Design, Project 1' to 'Project 1, Design' we get the following TimeSheet: