Ok, wow is there a lot to change here, let me delve into more detail, because I'm close to getting things done with only a few speedbumps.
I was using tztk's script to manage my whitelist, and it looks like getting the script and the mods to behave would not only be difficult, but redundant with other whitelist plugins available for bukkit.
So yeah, I got bukkit working with my server, I even have the init.d scripts working.
Now I need two things worked out and I will be good to go.
1) I need to get some essential plugins installed on the server, and I see no instructions on how to install one. How do I install a plugin?
2) When I fly on my server, it kicks me stating, "Flying is not enabled on this server"
*EDIT*
Disregard #1, I found their cleverly hidden FAQ:
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*EDIT*
Disregard #2, I found the settings in server.properties.
Thanks so much for everyone's help!