There are no ways for Empoleon to cover it's weaknesses with its abilities. The two abilities Empoleon has access to are:
Torrent | Boosts the power of Empoleon's Water-type moves when it's HP is 1/3 or less.
Defiant | Boosts Empoleon's attack 2 stages when one of it's other stats is lowered.
However, you can use some items to cover its weaknesses, Electric, Ground and Fighting.
First, you can use berries that halve the damage of these types of moves when hit by one once.
The Shuca Berry will cover Ground.
The Wacan Berry will cover Electric.
And the Chople Berry will cover Fighting.
Remember that these berries are only usable once per battle, except if you have Recycle (which Empoleon can't even learn) or someone Tricks one to you (which is way too situational).
Out of the berries above, I'd recommend the Shuca Berry (due to the higher frequency of Pokemon with Earthquake), but it's your choice.
If you want to be fully immune to Ground-type moves, you can also give Empoleon an Air Balloon. This will make it immune to Ground type moves until it gets hit by any other moves that it isn't immune to (everything except Ground or Poison moves, and status moves), after which Ground type moves will hit you super effectively as usual.
If you don't want to dodge the weaknesses, you can try using a Weakness Policy, which is a much better choice than the Cell Battery because
1) It will increase both Attack and Special Attack by two stages, rather than only increasing Special Attack one stage and
2) It will count all of Empoleon's weaknesses, not only Electric.
In Double Battles you also have the option of using the move Skill Swap Empoleon to give it one of the abilities that absorb Empoleon's weaknesses, like Motor Drive, Volt Absorb or Levitate.
Hope this helped!