How to get linker flags from KDevelop into Makefile

Hello all, I just took my first steps towards using KDevelop for the development of some software I'm working on, but I'm encountering the following problem: I've set linker flags in the compile section of KDevelop, and it works fine when I compile the project from within KDevelop. If however I just go into the directory, and run ./configure followed by automake, then those linker flags do not get taken into account, and a following make command will fail on the linking stage. How can I go from developing in KDevelop towards distributing this software to people that don't use KDevelop, and still expect them to be able to compile my software? Regards, Pieter Hulshoff