We used to have a well and found out that at the end of the pipe at the very bottom of the well, there was a filter of sorts that fitted on to the end of the pipe. It had become deteriorated and sand, dirt and whatever else was seeping into the bottom of the well and was going up through the pipe and contaminating the water. We had a problem with too much sand in the drinking water. I think the newer wells use a different way to pump water up. So it depends on how old your well is as to whether this would be useful information.
Also, if the water has a lot of rust in it, there is something they can attach to the well so that when the water goes through it, it gets rid of the rust before it goes through the water softener.
Water softeners usually have big drums of salt that the water is filtered through. You might want to check to make sure your water softener has plenty of salt.
A smell of rotten eggs can be gotten rid of by installing a chlorinater at the well before the water goes through your softener.