ok, my root directory looks like this:

/
/mail
/public_html
/public_ftp
/www
etc...

the absolute path for this directory is home/username/

where do i put Geeklog? should it look like this?

/
/mail
/public_html
/public_ftp
/www
/geeklog-1.3.1.1

if so, what's the deal with the public_html folder both in my root, and contained within the geeklog subfolder? EVERYTHING that's going to be accessible from a webpage on my server has to be in the public_html folder located in the root...

you have a folder named public_html inside your geeklog1.3.11 folder right?
take the contents of that folder and place them in your site's public_html folder. Your geeklog folder can stay where it is.
check your paths according to the install documentation and you're good to go.