No you won't have to pay an extra fee. They'd only know about it if they came out and did it. But since you said you can install the phone jack and run the cables under your house, I'd go ahead and do that. I forgot about the option of running things under the house because my house is built on a cement foundation so I couldn't do that.
So just buy a cheap router and do it yourself. If settings on your computer have to be changed, the router would include a little CD that would do that stuff for you.