[b]GIMP Version:[/b] 2.8.14
[b]Operating System:[/b] Linux
[b]OS Version:[/b] OpenSuse 13.2
[b]GIMP Experience:[/b] New User

[b]List any relevant plug-ins or scripts:[/b]
[i]Default installation only.[/i]

[b]List any ERROR messages you received:[/b]
[i]None.[/i]

[b][hr][/b]
When I have two layers and I paint, Gimp paints the layer I cannot see, not the layer I see. How come?

Is the proper layer selected in the Layer dialog?
Have a look at, Chapter 4. Getting Unstuck.

Hah ... Odinbc beat me to it. However, note that GIMP will operate on the selected ACTIVE layer, typically highlighted in blue. But that may not be the layer you can see.