I bought a everstart battery (part#25-3N ) from walmart. but its size is a little bigger than the orginial OEM battery.

Now I can't use the box which was covering the old battery. will this be a problem? I will try to put on the battery clamps.

No, it's not a problem. Infact, I had forgotten there ever was a box...mine had been gone for 8 years! Wow! If the battery is shorter you may have to modify your clamps somehow. I actually cut mine and rebent them, but some people use washers on the top so the nuts don't run out of thread.

I just put a piece of 1" plywood under the battery to raise it up. I've seen others put a piece or 2 of wood between the top and the strap.