I've been making a lot of improvements in this area lately, so if this is a brand new installation of cobbler I'd recommend you grab the master branch via github and use that instead. Specifically, I've been fixing:
* better apt repo support, to address the issue you mention above. Specifically now there are not separate repos for things like -security. Apt repos now have two new fields (apt_dists and apt_collections) so that you can mirror a lot more into a single repo. There are now also snippets to use these new repo configurations.
* templated late/early command scripts support
* debian network configuration (using the above late_command script support)
* per-interface network gateways (since deb/ubuntu doesn't really have a gateway of last resort configuration like redhat does, at least not that I've found).
Doing network configuration during the preseed is still a bit tricky, as preseed has a few hoops you need to jump through and doesn't always respect the d-i directives you specify. You'll probably want to continue to manually modify the preseed to use eth1 instead if that's the way you want to go.
If you do decide to use the master branch, be sure to back up /etc/cobbler, /var/lib/cobbler and /var/www/cobbler to preserve anything you might have done so far (make install/make webtest can/will reset some files to the defaults).