Get out your LED holders. Position the LEDs on whatever side of the Altoids tin you want, and make dots with a Sharpie on where you need to put each holder. Starting small, drill holes until you get the right size for the holder. Repeat for the other dots you made. Put the holders in the holes you drilled. Now place the LEDs in their holders. You should probably put electrical tape around at least one lead of each LED to prevent them from making contact.
My LEDs weren't really "snapping in" to their holders, and I drilled my holes a little too big, so I just used a little super-glue around the holders and the back of the LEDs (try not to get glue on the front of the LEDs because it dries white and will reduce the visibility of the light).