I'd make the call just to confirm what you are paying for. Don't mention you have a box unless they do charge, which I'm sure they will for that second unit. First box is always free. Even the £20 month cheap bundle gets a free box.
Wow, £45 is cheap. My bill for the lot was £117 until I renegotiated. So your first box (Sky+ HD) should be free. They do charge for the second though. The £99 box looks not to be Sky+ (recordable). I'd check ebay for a second hand Sky+ box. Of course you could call them to confirm all of this.