Unlike WebOffice 10R3 and previous versions, WebOffice 10.4 SP2 now only supports one data frame per map service (and further map document) due to Esri core software restriction. Therefore, create a number of map documents divided by the type (dynamic or static) or the use (globally used, project specific) of geodata, each containing one data frame.
Nomenclature
Try to avoid nonalphanumeric characters (other than spaces) in the data frame. The data frame name will be used in URLs which can cause problems when using nonalphanumeric characters. For better clear view it is recommended to use the same name for data frame and map document. (e.g. SampleProject_Cadaster.mxd containing the data frame "SampleProject_Cadaster").
Note: Also see the chapters Combine Dynamic and Static Geodata Properly, Split Up Globally Used Data from Data for Specific Projects for more information about the various types of geodata and how to provide them in different map documents.
Note: In case you have a map document with more than one data frame, see chapter Divide an MXD into Several MXD with 1 Data Frame in Each Document.