I am developing a mid-size e-commerce site. I say mid-size because I
am building it ontop of an existing site I own, and so will have
significant traffic from day one.

Anyway, my question is how can I set up my accounting so that I can
track and manage all of my orders? we are dealing with a few hundred
orders a day, and to manualy input all of those transactions into
excel or quickbooks, would take a dedicated staffer...There must be a
better way.

Dear bchlh-ga, 

There are a number of different ways to do this.

One is to use an e-commerce system that lets you download the
transactions directly into your accounting system. Many of the
shopping cart designers have included file downloads that let
you select the format from among,comma-delimited files, Excel files
or even QuickBooks files. 

The one I am using, 1automationwiz.com does offer that. 


The other option is to use an accounting system that incorporates
a shopping cart and website. Take a look at two systems - 

QuickBooks Online  
http://oe.quickbooks.com/addons.cfm

Here are some of the third-party solutions designed to 
work with QuickBooks.

Oracle's NetSuite - https://system.netsuite.com/ 
Working on an article recently, I interviewed a man who runs
his entire business using this product. They create his website,
provide a shopping cart that tracks inventory, records his sales
instantly into his accounting system. In fact, his deliverymen
can even enter status and bills of lading into the system when
they'd dropped off their orders - along with any customer comments,
new orders, etc. 

Customers can look up the status of their orders and log into their
account history. Vendors can log in the information on their shipments...
it will do anything - for a price.

It's so interesting that I am considering talking to them.

There's another option I am exploring - MemberStar
http://www.memberstar.com

It's also an entire site system - including customizable site templates, 
membership access at various levels, shopping cart - and financial reports!
You might want to talk to them, too.  

I find that the less time you have to spend doing administration,
the more time you can spend earning money - or enjoying the money you've earned.

I hope this helps?

Feel free to ask me questions. 

best wishes,

Your TaxMama-ga

Must be a better way.  Something connected to the order form.