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You can always take a look at the structure of existing packages on github. You will see that, whithin a package, .h files are in the include folder, .cpp are in the src folder, custom messages(.msg) and services(.srv) go to msg and srv folders, .launch and test files also have their respective folders. For example you can examine this package.

Regarding the problem you have with not being able to access the header variables, make sure that you have included the header files properly in your CMakeLists.txt