BabelMap supports a wide range of configuration parameters, most of which can be set from the Options menu. These options are stored in the Windows Registry for the current user (e.g. HKEY_CURRENT_USER/Software/BabelStone/BabelMap).
You may run multiple instances of BabelMap with different configurations simply by copying BabelMap.exe to different file names. Each differently-named copy of BabelMap will maintain its own configuration settings in the Windows Registry. For example, you might have two copies of BabelMap, one named BabelMap_Latin.exe which has font mappings optimized for the Latin script, and one named BabelMap_CJK.exe which has font mappings optimized for Chinese, Japanese and Korean. The configuration settings for these two copies of BabelMap will be stored in the Registry under "HKEY_CURRENT_USER/Software/BabelStone/BabelMap_Latin" and "HKEY_CURRENT_USER/Software/BabelStone/BabelMap_CJK" respectively. Note, you may rename BabelMap.exe to any valid filename you wish, and it does not need to include the name "BabelMap".
If you wish to run different versions of BabelMap on the same computer, it is advisable to give them different names so that they use different registry keys, and so avoid issues with configuration parameters changing between versions.