From the sounds of it (No pun intended) the sub is fine since it is not constantly running at max, therefore it is probably just a loose screw or something. The amp would look like a cube/rectangle encased in metal or it might just be and open amp with no case (components exposed).
You're right, it is a pretty tight fit so you might have a tough time reaching in but the amp should be bolted to the removable panel or at least close to it.
The system should still be covered by the two year warantee unless you open it up.
The back of the best buy bill/warantee states that as long as you have the bill/proof of purchase they will accept it. ""IF"" you don't have the box or other materials it came with they deduct a small amout from the money you get back or something like that.
There is still that small chance that the sub's "Voice Coils" (Copper wire coils) are rubbing against the magnet. Depending on what the humidity, temperature, and if it has been in the sun it may be damaged,causing the surrounding material holding the sub in place to be worn out causing a rattling sound, ( had the same problem with 20 year old speakers but your sub isn't 20 years old lol ).
Np with the help.