Hi,
it's little bit complex so I try to describe individual issues one by one.
Multiple configurations for one project
Unfortunately, in MCUXpresso IDE, there is a limitation, it's not expected to have multiple .mex files in the root of the project. However, its possible to workaround it. You can create/copy the second .mex file into the project root.
Then, anytime you would like to modify pins/clocks/peripherals of some configuration, you have to open the configuration you would like to modify using double-click it on the .mex file in the project view.

The downside is that the config tools do not indicate, which of the .mex you are editing at the moment. There is just IDE project shown in the toolbar. That's why you should always double-click the .mex file to get to Config Tools perspective to ensure the right project is edited.
Generating code to different folders
Second limitation is the sage of 'Update code' command which is currently limited to use the default 'board' project in project.
There an option specific for each .mex file where you can override the default code generation folder by custom path (ConfigTools > Configuration Preferemces > Output path overrides). However, I have learned that there is reported a bug in this feature and these rules are currently not applied when there is toolchain project detected (e.g. MCUXpresso IDE). After it's fixed, there will be possible to generate files to different folder from each .mex file.
The workaround for now is to use the Export command, where you can specify the target folder. The shortcut icon for the export is available in the Code preview window of each config tool:

Solution with MCUXpresso Config tools standalone
Alternative solution for the above limitation can be to using the MCUXPresso Config tools standalone application (https://www.nxp.com/design/software/development-software/mcuxpresso-software-and-tools-/mcuxpresso-c...).
If you are using the standalone config tools, you can move the .mex files into different folders and just open .mex file and edit them.
The 'Update code' command will produce output to the sub-folders of the folders where you saved the .mex file, but it can be overriden via the rules in Configuration preferences mentioned above.
Downside of this solution is that it will not handle dependency checks of the SDK components in your toolchain project this way so you have to ensure you have right files (drivers, middleware) in your project.
We are sorry for the inconvenience, we are preparing improvements to simplify these more complex use-cases.
best regards
Petr Hradsky
Config Tools Team