Add a product option
One-time fees, like set-up fees, have to be configured as product options. Product options are an advanced configuration which allows you to create bundles or to let the customer select from a variety of different options that will ultimately make up the final purchase. Use Product Options under Actions on the right.
Create product option group
A set-up fee can be part of a subscription. Therefore you can create a bundle with automatic selection that allows the user to subscribe only if he's willing to pay the set-up fee.
Add a product option to the group
After pressing Next, the bundle option group will appear. Clicking Add Option will open the product option screen. Inside section Create New Product, you can then enter a product name (e.g. Set-up Fee) and choose a format and set a pricing.
Adjust the product option
After creating the product option, you may want to tweak it a bit. For example, you can enter an explanation as a custom display. Click X to close the settings window and then Save (under Actions on the right).
Test the Result
Go to your testing links and review how the settings work in your store.