I assume you're talking about changing configuration options. It took me a lot of searching, but I finally recently learned how to do this.
First of all, use apt-get to download the source package, but don't let it compile automatically. Enter the source directory, then the debian directory inside it, and edit the "rules" file you'll find there to add the flags you want. It should be fairly obvious in most cases where the flags go. Then use dpkg to build and install the package.
Sorry about the lack of detail though. I neglected to take down detailed notes and I'm having to go by memory on this. You'll have to read the apt-get and dpkg man pages for how exactly to go about this.
I believe there's also a way to pass on compiler flags through the dpkg command line or an environment variable, but I'm not sure.
Edit:
Here's the page I got the information from. Go there for the detailed steps. Luckily I had it bookmarked.
