Probably the sanest way to handle this would be to create two orders per product type, each shipping with a different carrier to the same address. This also IMO makes more sense from a stores tracking perspective as you can handle each independently from each other.
To get you on the right track(since Magento is especially cryptic in this part of itself) you should read the Inchoo programmatically create order in Magento post and by the same author Programatically create customer and order in Magento with full blown one page checkout.
Basically as I see this going is:
- Get the customer order
- Itinerate through each product inside the order and split it up in two arrays for each product type
- Create a separate order for each product type and use the different shipping methods for each.
You will probably have to extend a some controllers OR do it the non-standard way and use helper functions for this, the hard parts will be integrating the payment/shipping modules inside your order process. Going this way will have you creating the full checkout process as the one page checkout Magento provides won't really work and is too much pain to get to work because of the way it uses AJAX.
Also another alternative is to hook in to Magento's pre-create order events and create the orders there using already defined order data split it up in two orders, but this is something I never heard or saw implemented at the moment so you'd have to do it "blindfolded" so to speak.
An easier approach would be to use a custom field that defines your product's shipping method, this way you just add that and don't care about custom orders. You just react with that, however tracking will become mostly impossible IMO.
