The Trainer tab is where you'll decide what sprite you want to use, what name you want to use, the message that appears when you win and the message that appears when you lose. There won't be a sprite for most of the Anime-exclusive characters but you can find ones for Misty or Iris who do have game counterparts. Making the winning and losing messages can be fun if you try something in-character; Carbarnet and a losing message about getting revenge as an example.
The Team tab is where you choose all your Pokémon. It looks like this:
On the left you'll be able to choose which Pokémon you want. In this one I've choosen Axew and nicknamed it Kibago. Underneath the nickname option I've given it a Focus Sash; it's here that you choose items.
In the top-half of the middle section is where you give your Pokémon EVs and a nature. The text boxes on the right are all filled with zeroes which means it has no EVs in those stats; this is a default. I've given it a Hardy nature in the drop down box which is a neutral nature.
In the bottom-half you can choose which moves to give the Pokémon, as well as details on the base power of the moves, it's PP, what effects the moves have as well as how that Pokémon learns the move (through levelling, tutoring, breeding, etc). I've given this Axew Dragon Dance, Outrage, Reversal and Endeavor to give it a fighting chance.
On the right you'll see options for IVs (called DVs in the picture), gender, Hidden Power type, happiness and ability. The IVs are all set to 31 at default and the Hidden Power type is Dark, which doesn't matter to me as I'm not using the move. The gender is male which is confirmed in the anime and I've given it the Rivalry ability as its ability isn't confirmed, so I can choose to give it that. I didn't go for Unnerve as it is a Dream World ability which aren't confirmed in the Anime. I've given it a maximum happiness of 255 as I'm sure Axew loves its trainer, Iris. I also haven't checked the Shiny tickbox as Axew isn't a Shiny Pokémon.
At the very top you'll see that Excadrill and Emolga are also in my team. Clicking on either of them will let me edit them individually. 3 of the spots are empty as Iris only has 3 Pokémon.
When you're done creating the team, click on Save and give the team a good, meaningful name. You're now ready to battle others with it.