Create a new empty project (file -> new -> project, empty project), choosing a project folder somewhere near the sources you are trying to compile (e.g. in the same directory)
Select project -> add files... to add the sources, which you will then see under the project in the "projects" tab of the management side bar.
Select project -> properties -> check this is a custom make file, press OK.
Then goto project build options to specify makefile commands for each target (you can also set global variable substitutions and pre/post build steps)
(You can add/remove targets in project -> properties -> build targets -- I am not sure whether the "Selected build target options" do anything when you specify a custom makefile, but I think things work pretty well if you have target name that match up with targets in the makefile. Would be great if source and target detection were automatic, but alas...)