I’m sure this has been discussed before, but with the new release I can’t tell what applies to the new version and what applies to the old version. How should I handle shipping charges in the following two situations:

1. The weights of our items vary from less than a pound to over 10 pounds. We currently offer free shipping in the continental US, but don’t sell international. I’d like to offer international shipping based on weight and destination. USPS Flat Rate Boxes will not work because of the varied dimensions of the items we sell.
2. If a customer purchases more than one item, how would I handle the shipping charges. For example, If a Customer buys one item weighting 1 pound and a second item weighting 5 pounds.

You can see the variation in item weights by look at this Shopping Cart category:
http://www.berrypatchgifts.com/shop/viewcategory.php?groupid=13

Does anyone have this same issue?
How do you handle it?
Is there a “work around”?
If I use PayPal Website Payment Standard will that make a difference?
Is there a third party add-on you’re using?

Right now there is no such feature in our software to accommodate what you are looking for. It is our goal to figure out a way to offer more expanded shipping options in either an upcoming release or with our 'pro' version due out later this year.

Just a note; better control over shipping costs is something I am waiting for as well. It will make things easier on me.....

Me too! From a half ounce pack of yeast to a 40 pound bottle corker, there is no way to just have one price for shipping. It just doesn't work that way in the real world.
Then you have to consider how far away they are also. That alone can vary the actual price considerably.