For dust spots on the neg, I'll often retouch with a soft lead pencil.

To avoid dust spots, don't use a changing bag. The changing tents, where the fabric does not contact the film or the holders are better, but a darkroom (or a dark room) is really the best.

I usually brush out my holders with a Kinetronics anti-static brush.

Other tips--

Wear a hat when you are loading. Some of that dust may be dandruff.

Store holders on edge rather than flat to prevent dust from settling on the slides and working their way onto the film when the slide is pulled.

Some people swear by ziplock bags, but some say that they cause their own static problems. I don't use them in general.