Applying Custom Product from Admin

2 Ideas:
1. You could add an additional Product Option like the "text style" which could be something like "text or logo". You would tack on the $3 if they choose logo but if they choose text then the price stays the same. That's one option and a much less time consuming one for you in the back end. It's only 3% of orders now but still takes time. This way the customer already knows all of their fees upfront. You would just need a way for your customers to send the file. :)

2. I add a box and a free product with all of my orders and I haven't figured out a way to simply add it to their cart without having to manually add it to the back end. Very time consuming so I know what you're going through. One day. :) But I simply added a few items which are only visible in the admin and then i can always go in and edit the orders before i ship them to include those items. It's just a matter of adding a Hidden Category and then applying those products to that category. Then those items will never be seen. So you could do this by adding a category which is "Custom Fees" and add products like "$3 digitizing fee" to that category. Keep in mind when you add items via the back end it's pretty time consuming. Like 6-7 steps/pages. Edit Order>Add products>Search for product>click radio button>accept>click add to cart> then it's finally added to the order.
I wish there was a "add sku" field and "qty" next to it with the "add to order" button, instead of all of the other stuff we have to do. ;)  This is why I suggest doing the first option because it'll save you those dumb steps in the end.

I hope that made sense. Let me know if you have questions.