Hi Dan,
I dropship and also have some products myself, so I have a combination of both..I let everyone know on the Ordering and Shipping pages that some products come directly from the vendor/manufacturer, so they know they might receive more than one package. I also have a tab on my product page with the information so they know upfront. It's also in the order confirmation email as well.
As for the shipping price, I find it's easier to just use one flat rate for everything. On some orders I might lose a bit, but on others I make up for it. It's too challenging to do it any other way for me.
Hope this helps :-)
-Lisa