To manually start any tools you want you can add them to the "Tools"-menu, but that will not save any open files.
The easiest way to do this would be to use a custm-makefile project (in your case) and pre- and/or post-build steps.
Just create an empty project, add all the files that belong to it via the context-menu in the management pane, open the projects properties via the context-menu, and chose this is a custom makefile (and the makefile name) at the first tab.
You most likely have to fix the make commands in the "Make commands" tab of the projects build options.
In the build options you can also add post and pre-build steps.
If you click the build, or rebuild-button the project-manager will save all files automatically.
At the moment, the makefile has to be in the projects base-directory, but I have a patch on my computer, that will make it possible to change the makefiles execution directory.
The patch is not (yet) tested on windows, but this might happen this evening and so I might be able to commit it today.