I have found that CP2K code do not read the normal Cartesian coordinates. Further there are a lot of options to make the input files suitable according to your need. Any help can be handy.
If I understand you question correctly, you can always use the TOPOLOGY section in CP2K as follows (and leave out the COORD section)
&TOPOLOGY
COORD_FILE_FORMAT XYZ
COORD_FILE_NAME geometry.xyz
&END TOPOLOGY
Now, you can simply use any gui interface (I prefer Atomic simulation environment and is really good if you like Python and want to have a little more control over things you can do) to make your geometry.xyz file. This xyz file should reside in the working directory.
Or, I don't know if you are looking for something like PYCP2K or related tools - see https://www.cp2k.org/tools
We have recently published a simple and interactive GUI that allows you to create CP2K input files. The program is called CP2K Editor, and it provides a user-friendly interface for both new and experienced users. The program is freely available on Github (https://github.com/avishart/CP2K_Editor) and you can find information about the program in the following paper: Vishart, A.L., Ree, N. & Mikkelsen, K.V. J Mol Model (2019) 25: 115. https://doi.org/10.1007/s00894-019-3987-6