Setting text formats programatically
You're going to want to create your new input format separately (probably in a module), assign it to the fields in your content type, then export the fields again and bundle in your module.  

Not knowing how complex your new input format is, best advice is to grab the examples module and check out the filter_example module for a good test case of how to create a new input format. 

Once you have the input format created, go back to your content type and under "Structure > Content Types > Manage Fields" set the default input format for these fields to your new input format and export your fields to your module.