directory changes HELP...

[ERICKSON,IAN (HP-FtCollins,ex1)]

Hi,
I just got put on a Linux project (and I'm not too familiar with Linux)
where I am updating a program package.  I have all the software changes in
place, but now I want to change how the command "make install" works.
Currently when I run "configure", its default prefix directory is
/usr/local.  I want to change this. how?  also, I want to change where the
"lib" directory goes and the a few others "glade directory"....

To get things to work correctly for me, I am running configure with several
flags like the following:   --prefix=NewPath, 
--libbdir=NewPath.

I don't understand how automake interacts with configure interacts with
configure.in and Makefile.am's  etc..............

Can anyone help me understand this mess and what I can look into doing to
change things so that I can just run "configure" and "make install" and have
things go into the new-correct directories?   

Any help greatly appreciated!!

Thanks
ian