Val,
I use Lifesaver and Quickbooks but they are used independently since there is no connection between the two. I am a small operation so I may not be representative of the most efficient way to do things.
I use Lifesaver to do all my pricing, tracking orders, customers. My main incentive to using it is the work order tracking as well as pricing updates from all the vendors.
I use Quickbooks to track everything accounting-related such as Sales, COGS, expenses and bills, inventory, etc. I also use it to provide invoices to my customers b/c I don't like the receipts that come out of Lifesaver. Quickbooks allowed me to customize it exactly down to putting my logo on the top. So as a result, after an order, I enter the customer info again plus the total price of the sale. I don't track any inventory except glass so when I enter an invoice from a vendor, it normally goes straight to COGS then. I would guess that higher volume operations would simply enter an end of day (or week or month) total into QB to update their COGS.
As far as Quicken vs Quickbooks, most businesses use Quickbooks since it uses double-sided accounting as opposed to single sided in Quicken. It is also designed around a business so it has the business terminology rather than in Quicken where you may have to sort of translate features to what you need. I use Quicken for my personal checkbook and it is 200x easier to use than Quickbooks but now that I got the hang of Quickbooks, I am really happy with it.
I can't give you a recommendation on how to use it since this depends on how your accountant would like to see it for tax purposes but this is what I've been doing. Feel free to email me if you have more questions on how I'm doing this.
Also, I took one of these free classes at HP.com to learn the basics of QB. After that, I was comfortable enough to learn the more advanced features. Here's the link to the classes:
http://h30187.www3.hp.com/courses/overview.jsp?courseId=2644
Good luck!
Lisa