When you launch the launcher for the first time, it will create a folder in you Skyrim folder called EnderalLauncher, close the launcher (important), then open the EnderalLauncher folder and go to system/config. There you need to open the conf.sur (txt-Editor is enough, no other software needed) - then set the InstallStat=0 to InstallStat=1.
Now the launcher thinks that you properly installed Enderal and will work es intended.
The only downside by doing it this way, is that you essentially killed your Skyrim, you have overwritten its files and didn't back it up with the Launcher as usual, so the only way to get back to Skyrim is erasing all Enderal files and integrety check Skyrim or just a complete reinstall of Skyrim (you still should delete all Enderal files before the reinstall in that case)