BabelPad 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/BabelPad).
You may run multiple instances of BabelPad with different configurations simply by copying BabelPad.exe to different file names. Each differently-named copy of BabelPad will maintain its own configuration settings in the Windows Registry. For example, you might have two copies of BabelPad, one named BabelPad_Latin.exe which has font mappings optimized for the Latin script, and one named BabelPad_CJK.exe which has font mappings optimized for Chinese, Japanese and Korean. The configuration settings for these two copies of BabelPad will be stored in the Registry under "HKEY_CURRENT_USER/Software/BabelStone/BabelPad_Latin" and "HKEY_CURRENT_USER/Software/BabelStone/BabelPad_CJK" respectively. Note, you may rename BabelPad.exe to any valid filename you wish, and it does not need to include the name "BabelPad".
If you wish to run different versions of BabelPad 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.