A "makefile", typically, contains rules for building something. You can't "run" it. You use the "make" command that will interpret the makefile and perform the actions specified in it.

So, I'm guessing your main confusion stems from what environment to use for what task. To build, using make and a makefile, scratchbox is typically used if you're not using some other setup.

To then run the application you either move it to the N900 and run it from there of you use the ESbox thingy (I guess, I don't use that nor scratchbox).