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The 2.6 kernel is newer and it's more likely you'll get more of the newer hardware recognized than a 2.4 one.
But it's ok to install with the 2.4 kernel and then apt-get the latest version from Debian.
Oh, and BTW, it's spelled k-e-r-n-e-l, not kernal.
I found it interesting that the Sarge install option for kernel 2.6x didn't seem to have support for my Perc4 RAID controller where the 2.4x version did. So I'm with the guy who mentioned something like, if it works, use it