Hi,
I am running Cumulus MX on a Raspberry Pi as well and there is no setting in the menus to set the cloud-base unit. It was there in the original Cumulus but is not in the MX version. However, no worry, there is a way to fix it.
Stop Cumulus MX from running
Using a text editor edit the Cumulus.ini file , and change the CloudBaseInFeet value to 0: This will give the cloud-base in Metres. (You will probably find its set to 1). It can be found about 3 or 4 lines from the bottom of the stations settings section.
Save the file and restart Cumulus MX again.
Let me know if it fixes it.