Ubuntu uses the m-a, too!
You probably have to create a new kernel.. Not so much a problem I think. I did that, too.
There's another command for this: make-kpkg. It creates the linux-image and linux-headers packages that you then can "dpkg -i" in the system. For this kernel m-a should find the headers. You still need to create a uImage to put into uboot as long as we cannot boot the kernel from the disk. I have some notes on this at http://oinkzwurgl.org/guruplug_kernel
I'm pretty sure that you can use make-kpkg to cross-compile kernels. But I've never done that.