Profiles
CSMMT by the nature of its design doesn't really need multiple profiles of configurations. As a result, it was built around the notion of an auto-saving registry based system. However, while in most cases there isn't going to be any reason to use profiles, I can think of a few cases where it might be useful. Consider for instance a case where a game uses macros such as Control 1-0, which are logical choices for Select Monitor 1-10 macros.. In this instance a user might want to make a secondary profile of macros instead of changing his or her normal macro configuration that they're familiar with.
Well, in afterthought multiple profile support was added at the last minute in a similar way to how it was implemented in AGS - Automatic Gamma System, another ComroeStudios product.. You can by command line tell CSMMT to use an alternative profile. The command line argument for this is "Profile=<profile>", where <profile> is whatever you wish to name the active profile. The default profile loaded if you specify nothing is ... "Default". It's recommended that you use the default profile for your primary so that you can use the start with Windows option in CSMMT. If you want to use another profile you'll have to create a shortcut yourself, as the start with Windows option will not add custom profiles to the loading arguments, and so will only load the default.
As an example of starting CSMMT with a custom profile for Supreme Commander, you'd make a shortcut such as "CSMMT.exe Profile=SupremeCommander" This will create a separate branch of configuration data for SupremeCommander so that you can have different Macro settings on an application by application basis.
Note that at the current time it's necessary to close CSMMT and restart it to load an alternative profile. This may change at a future date if CSMMT's users (you) consider it an issue worth improving on.