Yagarto managed make

Hi All
I've got a sam3s-ek that I'm keen to try, and following the yagarto 
instructions for setting up the environment - I'm new to eclipse and arm 
- coming from mega2560/AvrStudio4.
Yagarto instructions works very nicely - and very thankful for the 
detailed directions - and I've compiled a test project and getting ready 
to download it via a SAM-ICE (Segger J Link JTAG 20pin!).
Now I'm trying to add another file and get the make file to be 
regenerated,
I don't seem to be able to set the environment to a managed make.
I've spent about 4 hours learning a lot about eclipse and all the work 
that has gone into yagarto - so very impressed overall.

So mystified as to if i'm missing how to do a "managed make" ?
More specifically - as a trial to get my feet wet - I want to port the 
demo example (Kiell) - so there will be lots of files and dependencies 
being added and I would have thought eclipse or make would have been 
built to handle a core build function.

many thanks for any insights
Neil