since the Soekris has no monitor or keyboard.
You can use the serial console.
Is there a way to install without using the Debian installer? Or is there some way to run the installer on my laptop and have it install everything on the compact flash card (and not mess with my laptop's OS of course)?
Yes, we use debootstrap with a custom kernel. But we use the ARM port of Debian. -- http://arhuaco.org http://emQbit.com