Example if I set a shipping fee of $7.99 and when user adds product1 and product2, the shipping fee is added to product1 and product2 for a total of $15.98. Is there a way to set the shipping fee for the whole order which in this case would be $7.99 total.

Hello Danny,
Can you please provide a link to your page?

Here is the link dannywebdesigns.com/store/

The shipping fee is $4.99. I would like to make the shipping fee to be the total amount of $4.99 per order not per item.

I see what you mean.
The shopping cart shipping is applied for each item - that means that if you add shipping cost of $4.99 to "item1" then this price will be applied to the "item1" regardless of the quantity of items purchased.
If you add shipping cost to "item2" it works the same way, but on the checkout PayPal calculates the shipping costs for the different items.
You can just leave the shipping field empty and set it in your paypal account.