Linux Loaded on 486...what now

In looking over the packages I need to add to equal the workstation install,
I've decided the best option would be to just go back and do a workststion
install. The question I have is this - all of the MANY instructions I've
read on LINUX installation recommend partitioning the disk something like
/100M , /usr 200M , /usr/src200M , etc.; what then is the drawback(s) of
using the very basic filestructure created by Workstation install? Also,
when you do partition the disk and do a custom install, how does linux
distribute the installation? In other words, do the various packages and
components get placed on their respective partitions automatically? Do you
have to relocate them later?
Patrick