How to make a CP2K input file with Avogadro?
If you look at the CP2K website, you'll see that the coordinates are only a small fraction of the input file. Most of it is text describing how a calculation should be run.

The key parts from a coordinates perspective look like this:

&amp;CELL
  ABC 12.4138 12.4138 12.4138
&amp;END CELL
&amp;COORD
  O      12.235322       1.376642      10.869880
  H      12.415139       2.233125      11.257611
  H      11.922476       1.573799       9.986994
&amp;END COORD


As it looks, these are the Cartesian coordinates of the atoms (in regular space) and the unit cell vectors. You can either save the file in .XYZ format or use an input generator like GAMESS or Gaussian to get these coordinates.

If you want a periodic boundary calculation, you just need to estimate the bounding box. You can do this manually, or you can go to Crystallography | Add Unit Cell and then tweak the volume. In Avogadro v1.1.x, you'll see the ABC lattice vectors needed for that CP2K block.

As it might seem, Avogadro2 will be v2.0 of Avogadro. It's still in development.