I've never used TL myself Josh, so I'll let those with some experience clue you in with that one.
As for setting the shipping price in ebay. You can add the item specifics in your listing and use a postage calculator for the customers to do their own quotes.
I would always test run this option, just to make sure the figure the calculator was throwing up were accurate.
You can set a flat rate if you want to. It really depends on the type of products, and the shipping locations you are covering as to the best option I would suggest.