[jillsybte]

OK, I'm a little tired so I'm not sure I'm thinking clearly... Do you mean you have an actual shipping method that's free and then another method that's not?

I have a similar situation to yours in my store. I have some items that drop-ship and the rest I ship via various methods. So I set a freight charge on the drop-ship items and then also use the setting to NOT calculate shipping on items with freight charges. Then I select all shipping methods for the drop-ship items so that they won't interfere with the other items in an order. There's also the option to choose "Free Shipping" when modifying a product. I don't use that myself, but I think that allows you to mix free shipping items with items that ship for a fee.

Your best bet is probably to contact BCSE. They make tons of mods and use X-Cart themselves so they can probably help you figure out what would work best for your store.