How to attach a rune to a silver sword?

There are two types of runes: temporary and permanent.

Temporary runes (Perun, Svarog, Vodon) are consumed on use and give a bonus to your weapon for a period of time (I believe 24 hours). To use them, just right click and then select your sword (note that they can be used on either your steel or silver sword).

Permanent runes (Sun, Moon, Earth) are used to create a new silver sword. To do this you will need to collect at least 3 permanent runes and then talk with a blacksmith. You will then be presented with the usual trading UI, where you will be able to see the sword(s) that can be created with the runes you are carrying. Each permanent rune will bestow different abilities on the resulting blade, so if you bring 5 permanent runes, you'll be able to see a number of swords created by the various combinations and choose the one you want.

Don't worry too much about saving up your runes for the best possible time, since you'll eventualy earn a sword that is much better than any you could create. See What Rune and Meteorite combinations offer me the most effective blades?

You need to find a blacksmith in any city.

More on runes