Filegroup mappings allow you to compare databases that have different filegroup structure. for more details about filegroup mappings, see SQL Schema Compare Filegroup Mappings.
Below is the xml fragment generated for this filegroup mapping scenario:
<FileGroupSettings>
<ComparisonType>ByMappings</ComparisonType>
<Mappings>FG_SOURCE_1:FG_TARGET_1;FG_SOURCE_2:FG_TARGET_2</Mappings>
</FileGroupSettings>