Delete your unit and start from scratch.
When you duplicate the unit,
do not duplicate the actor unless
you want to edit it, for example you want this specific unit to be larger or thinner than the average DT. If you want to do this, I can't help you. But if you don't care if it uses the original actor for the DT,
do not duplicate the actor. This problem will cease to exist.
The green lines
indicate something that exists souly in your game, and will not carry onto another game in the GE. For example, if you edit a barracks, it will become green to indicate you've changed it. However if you make a new map, it will be blue again.
What you need to do is right click every green box and select "use parent link" or something along those lines. Then go and delete whatever it is you've made so you don't get confused in the future (the 'link' to the object that was greened out).
As for builders.. well it is MUCH more difficult than the WC3 version, but can be MUCH more better in a lot of ways.
The way a builder works in this game is rather simple; command cards. Create a custom image (if you want to, that is) or use a pre-existing one. Place this image on the command card (usually at the bottom left). For Command Type you select "Submenu". Then set the "Command Card" field right below it to a number of your choice. For the example I will use #2. After you are done this, go to "Command Card" at the top and select #2. Place the abilities (build abilities) in the places you want and make sure you have a "Cancel Submenu" ability somewhere so they can get out of the building menu.
Essentially how the building operation goes now, is an ability leads the user to another command card which contains all the building abilities to create whatever it is you want.
Unlike Warcraft 3 where you could just say "okay, they can build this this and this" you need to actually create a build ability for each and every building / unit that you want another building / unit to be able to make.
So for "Build Marine" it has its own ability. For "Spawn Drone" it has its own ability. For "Build Pylon" it has its own ability, and so on and so forth.
You should be good to go now. It's been a little while since I've done this kinda stuff, but if you fittle around with the knowledge I've given you, you should do just fine.