Im not seeing any problem here. Youre not going to run out of room
anytime soon. Take a look at mine:

wadesmart@wadesmart:~$ df
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/sda5 9614116 4849764 4275980 54% /
tmpfs 4129240 0 4129240 0% /lib/init/rw
varrun 4129240 128 4129112 1% /var/run
varlock 4129240 0 4129240 0% /var/lock
udev 4129240 172 4129068 1% /dev
tmpfs 4129240 9576 4119664 1% /dev/shm
lrm 4129240 2192 4127048 1%
/lib/modules/2.6.28-18-server/volatile
/dev/sda1 482214 126663 330652 28% /boot
/dev/sdb5 74407740 47208120 23449652 67% /data
/dev/sda7 30965504 14089384 15303364 48% /home

As for where files are put when you install something, the way linux
works in general is to make sure you can keep different copies of the
same file, a older copy for this program and a newer copy for that
program - and have it all work together. I dont think I would try to put
everything in locations myself. Just let the install do it.