If the formats are different, you may want to keep the program-star tables separate. In any case, you should keep standard, constant, and variable stars in separate tables. Then you just enter the names of the different tables one by one, as you run the planning and reduction programs.
A more convenient way to handle multiple files is to make a catalog, and then just supply the catalog name. Only stars of a single type (standard, constant, or variable) should be kept in the same catalog. At present, only the reduction program can use star catalogs.