Does MyDefrag have a GUI?
For a screenshot see the MyDefrag homepage.
The window has more facilities than JkDefrag, but does not have all the facilities of the JkDefrag GUI by Emiel Wieldraaijer. There is no similar third-party GUI available for MyDefrag, yet.
Also, do I install it over JkDefrag or in addition to JkDefrag?
I am still confused about why the root drive has moved to e:, this is my backup drive. Wouldn't the root drive be on c:?
The boot disk is usually the C: disk, but it is possible to select a different disk when installing Windows. JkDefrag (and MyDefrag) do not care and do not change anything about boot disks, so whatever has happened on your computer cannot possible have been caused by JkDefrag.