The whole autogenerated configuration is stored in $HOME/.cuterc. This is a python file where the special variables of the built-in python interpreter of CUTE are held. Most of these can be configured with the 'Options > Configure CUTE' menu item. It is possible to modify the rest of the variables manually: load the file with 'Options > Show .cuterc file', adjust the values of any of the predefined variables, and then run the file using 'Extra > Run current file' (you cannot just Save the file as it would be at first ignored, and then overwritten when CUTE exits). All config variables are defined in python modules. There are 4 modules: general, edit, view and lang. The .cuterc file will execute $HOME/cute.pre_config (if it exists) before any options are set. After setting all options, .cuterc will execute $HOME/cute.post_config (if it exists).
Therefore any user configuration should be placed in either cute.pre_config or cute.post_config. Put definitions of new commands in cute.pre_config if they are to be configured in .cuterc.