Thanks for the reply, Tim. I think I figured out how to do it.
The problem is that you have to configure C::B for the right target. By default, C::B has "debug" and "release" as targets but those targets do not necessarily match the ones your Makefile needs.
So, the first thing is to go through your Makefile and figure out what kind of target you need. In my Makefile, the last two lines define the targets for PC and Mac, respectively:
program:
avrdude -p $(AVRDUDE_TARGET) -c stk500v2 -P $(AVRDUDE_PORT_WIN) -e -U flash:w:$(PRG).hex
install: hex
avrdude -p $(AVRDUDE_TARGET) -c stk500v2 -P $(AVRDUDE_PORT_MAC) -e -U flash:w:$(PRG).hex
Since I'm building for a PC i need to target "program":
1. Go to "Project" -> "Properties" -> "Project Settings"
2. Check the name of your Makefile (mine says "Makefile" ONLY, without specifying its home directory)
3. Select the box that says "This is a custom Makefile"
4. Go to the tab "Build targets" and on the list of targets ("Build" and "Release" should already be there) add a new target named "program"
5. Press OK
6. Back to the project window, make sure that the "Build target" drop-down menu is set to "program"
7. Build your project, and BINGO! watch the STK lights turn on as the AVR program is uploaded to your STK500, ready to be tested.