You can scan your slides more easily if you store them in plastic viewpacks instead of boxes. Viewpacks are plastic transparent sheets with pockets to hold each slide. The 35mm packs usually take 24 slides per sheet; the more expensive kind have a dust cover. They can often be hung in a filing cabinet like suspension files.
For safe storage, slides should be kept in a cool, dry place - not the attic or the cellar. Heat and humidity are the enemies of colour dyes in slides and prints.
Clean dusty slides without scratching by using a soft camel-hair brush, the kind that's used to clean camera lenses. Dust lightly and gently, starting from the centre of the slide.