Before anything else make sure you double enabled the mod(s). The reason why you need to do this has nothing to do with Machiavellis coding, rather how the CIV BE modding was made by Sid Meier themself.

You need to enable this mod twice for it to work correctly. To do this:
Select all the mods you want and click next
Don't click start game, instead hit escape to go back
Click next again, this is the second time enabling the mod
Now you can start/load a game and it will work correctly

If you started a game with the graphics glitching you should make sure the BE process did not get stuck. If you just restart BE you will most likely hit the same problem again even with double-enabling and when starting an unmodded game.

To do this you have 2 options:
1. Start taskmanager (or equivalent program), go to "processes" and check if there is any process with CIVBE mentioned. It is usually in the top 5 processes and takes up more resources than the other background processes. Click on the CIV process and select "end process" and that should do it.
or just simply: 2. Restart your computer.

If the above methods did not work the next likeliest cause is mod conflict. If you are using other mods that change models (ie. changes what units and other stuff you see on the map) this is likely to happen. Mods that just change texts and game mechanics are not likely to screw up the graphics but might cause other more subtle and sometimes hilarious problems.

To eliminate mod conflict as a probable cause do this:
First disable all mods except Echoes of Earth and see if you can start a new game (remember to double-enable!) without any problems. If the graphics still do not work try starting a new game without mods: if the graphics are still wrong read the previous entry as the BE process most likely got stuck.
To find out which mod is the conflicting one try enabling just Echoes of Earth and one other mod. Remember to double-enable every time you start a new game. I know this can be a laborious process when using several mods. Try starting with the mods that change the most game elements, especially ones that change the graphics.

I will add some more obscure fixes later when I have time to browse through the comments section. In 90% of the cases the fixes above will make things work. If they do not it is more likely that you misunderstood some step or made some other human error. Don't worry, this happens to everyone.