Hey coomera I'd be happy to help!
First of all, it depends on if your products are coming from the same supplier or not. If they are coming from the same supplier, they may ship them together. However, if they are coming from two different places, then yes they will arrive separately. I would not consider this an issue as it's quite common for marketplaces to source products from different locations. When I order numerous items from Amazon, they normally come separately unless some are coming from the same fulfillment centre.
Second, in regards to freight charges, you should not have to pay any. The only fees you need to consider are the shipping charges. You can select the shipping option you'd like to use at checkout. Here is more information on dealing with shipping charges and how to work them into your product price. Hope that helps.