The calculation of the final shape and motion for objects in messiah happens in several stages. Throughout these stages your Modules have a chance to contribute to that shape or motion. The stages in processing, as illustrated above, are Keyframe Motion, Post Motion, Pre IK, Post IK, and Post Displacement. When each of these stages is being processed each Module will be given a chance to contribute in turn. Processing for each stage goes in the left-to-right order of messiah's modes (e.g. Animate Mode then Compose Mode then Setup Mode etc.). Each Module type will be called when it's associated mode is processing. For example Effect Modules will process when Setup Mode is processing, Customize Modules will process when Customize Module is processing.
The order that each Module of a specific type will be called depends on the Module type. In some cases the order is very important to the user, and they have the ability set the processing order by arranging items in a list. Effect Modules are a perfect example. Users will often need one Effect Module instance to calculate after another Effect Module instance has calculated. The user can easily arrange each of the Effect Module instances in Setup->Effects. The Effect Modules will process in the (top-down) order that they are listed.
Non-Instance Based Modules will always process in the alphabetical order of the Module's names. For that reason the user cannot re-order the processing of these types of Modules and therefore it is not advised (though not illegal) to process animation in Non-Instance Based Modules. Function Modules are an exception to this as they are called by instances of variables in Command Mode. The user is free to re-order the variables and thus is free to alter the processing.