Good day again :)
There had been a kind of muddiness in the steps in how entry file is set in a assembler project in Atmel studio. Here is what happens by the way.
When you create a new Assembler Project in Atmel studio 6.0, a default .asm file is added to the project and is set as an entry file. The entry file for the project could be found in the <EntryFile> element of the project file (i.e .asmproj). The entry file is the one that is passed on to the underlying assembler. So all the rest of the files should either be included using the .include directives or specified in the Project -> Properties -> Toolchain -> General -> Include Paths.
To change the entry file for a project, right click on the file that you want to set, and click "Set as entry file". Save the project and click "Build". Now the build command line should use the lastly set file for assembling.
Have a good time with studio.