Are there any deals to trade my 64GB iPhone SE for the new 128GB that Apple announced? I'm paying a monthly fee for my SE since last month?

Or would I have to pay for the new 128GB version outright if I decided to get ti? As of yesterday, Apple stopped making the 16GB and 64GB storage options for the iPhone SE and instead will be making 32GB and 128GB storage options for about the same price as the now former storage options.

You would have to pay for the new phone out right. The only way to get an upgrade like you want, would have been to return the lesser phone during the return period and paid the restocking fee, plus the difference between the two phone, during that time period (normally 7 to 14 days).