How to organise content to get the most out of SEF Advanced ?

If SEF Advanced writes URLs according to section and category like this:
www.domain.com/section/categoty/article/

Then what's the best way to organise my content so that I that I get a nice URL ? EG

Home
- Intro
- Terms & Conditions
- Recommended Links

Products
-Product 1
-Product 2
-Product 3

eBooks
-Title 1
-Title 2
-Title 3

A website that I just used SEF Advanced for was a simple site like this one and I used duplicate Section and Category names, which then looks awful in the URL. It's not possible to leave out the Section so what's the best way to organise this content so that I don't have duplicate section and category names ? Thanks...

Perhaps a generic section name like blog or go ?

go\products\product1
go\products\product2
go\products\product3

go\ebooks\title1
go\ebooks\title2
go\ebooks\title3

I have a somewhat related question.... My search engine traffic is beginning to grow and I am at a point where I would like to reorganize the layout of the Sections and Categories.  I think I already know the answer to this question but I'll ask anyway.

If I create a new set of Sections and Categories and begin moving my content around, I assume that the old search engine "links" will not find that content and I will be "punished" in the search engines.  One way around this is to have duplicate content I guess but the search engines also frown on that.

Does anyone have any ideas on how to do this?  Should I just make it a gradual thing?

Thanks for any ideas!

You can setup redirects in .htaccess manually to redirect requests to links in old sections to new ones.