subsite setups – 'best practices' questions

I have installed wp3 while keeping my html site mostly intact so I have a couple of questions regarding subsite setups because I’m more familiar with files vs DB mgmt.
If you look at my blog ( https://www.humantrinity.com/kenji ), all menu items go to my html pages. It’s the best I can do within my limited skillset. So…

1)re: Home
– can this be pointed to a html file located in the root & how

2)re: Fileupload Url
– could I point all sites to mydoamain.com/wp-uploads/site<x>

Also): doc or url
– is there a doc that explains (line by line)
‘Site Options – WP options (wp_12_options)’

Thanks!