Defeating Final Evolution Pokemon
Which is one of the main concepts to win a game, prepare your pokemon so that they can do massive damage and dominate the scenario (either by evolving it or get it ready with necessary energy cards). 

Since we are talking about theme decks here, cards and scenarios are limited which is really beginner-friendly. Each expansion (in your case, Ultra Prism) comes with 2 theme decks normally (which they balance out the odds of winning between them so they both will sell), each has it's strenghts and ways to take over the game. 

There are a few ways to "comeback" in the game playing any mode, unfortunately (and fortunately at the same time) in Theme mode ways to win is limited to setting up your Over Powered evolutions and swiping your oponents actives. One way to comeback in themes which I have noticed is sacraficing some prizes and Pokemon until you prepare a Pokemon that could take out your oponents active. 

Basically, while your opponent got their active evolved and ready with energies and is swiping your actives and taking prizes (he is 1-hit KOing your active Pokemon), he/she is probably "over comitting" on his active Pokemon, which they have spent a few turns only attaching enery cards to that pokemon and probably do not have other Pokemon prepared on their bench. 
You can take the opportunity to stall by giving him the turns to KO your some of your Pokemon while preparing 1 Pokemon to fight against his "OP" Empoleon. E.g. have your garchomp set with a Cynthia in hand so you can KO his Empoloeon with 200 dmg.

Try to get the cards you need to set up powerful attackers while your oponent is putting all his eggs in one basket, by optimizing usage of trainers and supportes you have in hand.

You need to calculate your sacrafices and chances, and give your best shot. There have been many times where games were turned from 6-1 prizes to 0-1.

I'm no pro player but hope that helps : )