In a multireference alignment [MRA] project, each particle will be aligned against R different templates. Multireference projects are mainly used to incarnate the Multireference analysis approach for simultaneous alignment and classification.
The process of multireference alignment
If you have R references and N particles, each particle will be aligned against all the R references. The particle will produce R different cross-correlation scores and R different sets of alignment pararameters. Thus, Dynamowill produce R different refinement tables, each for one reference channel.
Each particle will have a single reference yielding the maximal cc score.
The fact that you can define alignment masks and classification masks separately in a project is specially useful when running MRA projects. Very frequently, you want to use a wide mask that includes enough signal to drive the alignment, and a smaller mask, defined on the region where you expect or want to check for structural heterogeneity.
Introducing project elements (template, tables) for MRA projects is slightly different than introducing them for single reference projects. You can use a .sel file, or pass a folder, where files need to stick to a given naming convention.