OK, so heres what happened.
I used winUAE to add a folder/directory, then boot from the install disk from a 2.05 set (using a 2.04 ROM as it was the only one i had and 3.1 was bitchy about installing an older version of workbench). I then proceeded from step 21 of the guide that i found and then it seemed to install successfully. I ejected all workbench floppies from winUAE and boot again just to test, and it worked perfectly in winUAE. So this part seemed to go OK.
However, at this point im unsure what to do next (or what im forgetting to do next). I place the CF card in its current state into my PCMCIA adapter, put it in the amiga and turn it on, and its as if it wasnt there. am i missing something?