Emacs 23 - how to use flymake in a non-trivial project?

[Geralt]

Hi,

my C projects are using the autotools und to keep my source
directories clean from temp file I always have a build/ subdirectory
in which I run ../configure (actually I don't run configure all the
time, but that's the way the dir is initialized) and then in this dir
make -k to build my project. Is there a way to tell flymake the
command it should run for all .c/.h files below a directory?
Currently I can't use flymake because it can't find a Makefile for my
source files (because it only looks into the (sub)-directory).



Thanks,

Geralt.