You can use set_source_files_properties to add COMPILE_FLAGS for myprogram.cpp. For example:
add_executable(MyProgram myprogram.cpp)
# Add the -std=c++11 flag as an example
set_source_files_properties( myprogram.cpp PROPERTIES COMPILE_FLAGS "-std=c++11" )
target_link_libraries(MyProgram MyLibraries)
If you need those flags for all source files in the MyProgram target, you could use set_target_properties with the target property COMPILE_FLAGS:
add_executable(MyProgram myprogram.cpp)
# Add the -std=c++11 flag as an example
target_link_libraries(MyProgram MyLibraries)
set_target_properties( MyProgram PROPERTIES COMPILE_FLAGS "-std=c++11" )
Update: To remove a single property, you can first get all the properties and manually remove the offending flag from the list. For example with get_source_file_property:
get_source_file_property( MYPROPS myprogram.cpp COMPILE_FLAGS )
STRING( REPLACE "/MP1" "" MYPROPS ${MYPROPS} )
set_source_files_properties( myprogram.cpp COMPILE_FLAGS ${MYPROPS} )
However, I would recommend splitting your source files in two. One with all the source files with the \MP flag and another with only myprogram.cpp