Installing programs in root vs home partitions?

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http://askubuntu.com – I'm a new Linux user and a Windows convert. I tried Ubuntu (Dapper Drake) a few years ago and liked it quite a bit, and I'm in the process of installing Xubuntu 13.10 along side Windows7 on my brand new SSD! At this point, Windows is still being installed because I need it to be, but Linux is getting installed because I want to use it! I've done quite a bit of research and I've toyed around with Linux before, but I'm still a newbie and I have a few questions concerning partitions and program installations.. My new SSD isn't huge (120GB Samsung 840 EVO), and I'll be using my old 800GB HDD as a (HowTos)