You won't be able to load saved games from NE with the normal game, and I would doubt you can load saves from the normal game with NE.
If you're trying to completely get rid of NE now, I'd uninstall AoE3 with Revo Uninstaller (it's freeware) and then I'd browse to your Age of Empires III installation location, which will be in one of these places, depending on some variables:
Retail or GFWL:
C:\Program Files\Microsoft Games\Age of Empires III\
C:\Program Files\Microsoft Game Studios\Age of Empires III - Complete Collection\
C:\Program Files\Steam\steamapps\common\Age Of Empires 3\bin
And if your operating system is 64-bit, change "Program Files" to "Program Files (x86)".
If those paths are all empty of files, then go ahead and install again.
If this is an issue with getting something to load in NE, I'd post at their forums: http://www.ne.elpea.net/forum/portal.php