Accounting: Shipping 101 Charged vs Actual

Question for the smart people out there....
How do you handle Shipping/Handling accounting?

Lets say I sell a Widget I bought in bulk for $1.00 and sold for $10.00
And I charge a flat fee of $5.00 shipping.
So for this single order, the customer paid $15.00

Now, breaking apart the shipping:
I have a box that cost me $1.00, and this package actually cost me $3.00
($1.00 profit in shipping in this case...)

Recap:
($10.00 - $1.00) = $9.00 profit in the product.
($5.00 - ($1.00 + $3.00)  = $1.00 profit in the shipping.

How do you keep track of your shipping profit/loss for tax purposes?

I don't think this app naitvely allows us to enter the shipping actuals right?  
So are you keeping track of this somewhere else?
How is this done in a real world online store?

Thanks
Rob

We use Quickbooks for our accounting software. When we receive an order over the internet we enter the order into Quickbooks and separate the freight from product. We have a Quickbooks account for outgoing freight and have our charged shipping cost go into the account. Then when we get a bill in from the freight company we enter that into the same account. This will balance out with a + or - amount. That would be your profit or loss.

Thanks... so you don't keep track of shipping (actual cost) on a transactional level but rather more of an end of month "charge".

There is no way to keep track of the actual shipping charge on the transactional level right?  (From within the webapp, not quickbooks...)  Right?

Thanks,
Rob

I have not found any way of doing that in nopCommerce. It is something you would have to do outside in your accounting software. I do now that nopCommerce has a mod link to Quickbooks. I have not used it yet. I have also seen that their are others that have made mod links to Quickbooks. I figure I would wait until version 2.0 is out and after updating I will look more into the links.

We have an item in Quickbooks that is for freight and is linked to our freight account. That way we can keep track on am order bases.

I also do not like the Delivery button on the shipping tab. To set an order as delivered you have to go to the order and do so. These means that you have to track every shipment to know if it is delivered. I skip this and just leave it as shipped.