You don't actually USE anything.
To use a trainer, simply drag it onto your playmat, and your opponent will be able to see that you've played it (both by seeing the card on the mat and by seeing "xxx plays bebe's search" in the chat box. And then use it's effect (for instance, if it's a Bebe's, put a card from your hand on top of your deck, search your deck and put a Pokemon on the playmat, and then into your hand).
For attacking, just say "flash impact" in the chat box, or click on the card, and from there click on the attack name, which will put "Luxray - Flash Impact" or something of that sort in the chat.
The program does nothing for you except flip coins and randomize cards. You have to apply damage, use Powers, Bodies, remember effects, play cards, etc. by yourself.