It's the same word really, when used on its own. In spoken language you won't really her the difference since the consonant sound is often dropped.
When in doubt, use "NED" and you will very rarely be wrong.
However, I would guess that "ner" will replace "ned" in the same way "ned" replaced "never" in a not so far future,
I think my feelings towards the pair NER <> NED would be similar to how my great grandmother felt about NED vs NEDER.
But, it's not that simple when it comes to compound words.
Most of the times, you can use either word, and the meaning will be the same.
- nedåt / neråt
- nedvänd /nervänd
- nedtryckt / nertryckt
- nedsänkning / nersänkning
Sometimes the meaning is different:
- nedslagen = feeling depressed
- nerslagen = to be beaten to the ground
- nedsättande = demeaning
- nersättande = to put down
And sometimes the word doesn't even exist:
- nedfart = Piste / Ski Run
- nerfart = xxx