The phrase bottom end refers to the engine crank-case. An engine is comprised of a top end, which is the cylinder, cylinder head and piston, and the bottom end. Parts contained within the bottom end include the crank, engine bearings, oil seals, and any transmission an engine may have.
"Bottom end" is also sometimes used interchangeably with "low end." Definition depends on context, which is why it's important to pay close attention in moped-related conversation, especially conversations involving performance.