A rune does nothing while it sits in your bag. It has to go into a spell.
Eopens the spell editor. Drag the rune onto the graph, or click the rune and then click a socket.
Where you attach it matters. A rune hung under a trigger modifies that trigger, not the spell above it. That is the whole game.
Two limits, shown in the editor: sockets are how many runes fit, focus is what they cost.
A second copy levels one up. Take a rune you already have socketed and the duplicate can be spent in the editor to raise it, up to level 3 — stronger numbers, no extra socket, but one more focus each time. Cards that can do this are marked ↑ LV 2 on the level-up screen.