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I am using the second option that you have mentioned.
Firstly I can not install all my content as it uses too much space and I am not going to use everything. Sometimes I do want to get rid of something from my hard drive or I want to replace something with a newer or other version. Because I install everything now in it's own runtime I can at once uninstall something or add to it or whatever.

You should look at the following thread. I explain how to use file compression inside Poser to compress your files. It saves gads of space! 

http://www.renderosity.com/mod/forumpro/showthread.php?message_id=3169372&ebot_calc_page#message_3169372

Using external runtimes and file compression I managed to use a 40 gig hard drive for 3 years.

Making every single package that you install into a separate runtime is well... odd.  I only know one other person who does that and that is only because of not understanding the method of setting up a runtime for a "theme" and thought that every character or clothing or texture package that is installed had to be it's own runtime.

"It is good to see ourselves as others see us. Try as we may, we are never
able to know ourselves fully as we are, especially the evil side of us.
This we can do only if we are not angry with our critics but will take in good
heart whatever they might have to say." - Ghandi