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Layout Question

I'm trying to install the 2.2.18 kernel into a Debian install.
I'm not using the Deb binaries for a couple reasons, but I got into a jam..

I'm used to Slackware.  If you want to change it, you edit the file
directly.  Debian doesn't seem to do that very well.  Lots of warnings
about not changing files..

According the my previous experience with slackware my /etc/modules.conf
file should consist of something like:
alias cs46xx sound
alias eepro100 eth0

and really nothing else.
In Debian, I have many lines and many aliases and when I try to load a new
kernel, the modules won't load...
I need to tell Debian that there's a lot of files/modules I have no
intention of using.
What's the tool(s) to do that?

I'm afraid if I edit the /etc/modules.conf directly, the installation will
get mad.

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