If you haven't figured it out yet-
1- once in team builder the first screen you see is the screen for your name, info, your avatar(they call it image), the auto messages when you win/lose, and the graphics you want to use.
- Name- Self Explainatory, just enter what you want to be seen as.
- info- when someone challenges you they will see your info. If you like special circumstances to be enacted when battled(such as no skarm-bliss) you can put it here.
- Avatar/Image- meh... you know this...just pick one you like
- AutoWin/AutoLoss- Enter what you want to be said in those conditions.
- graphics- If you want your pokemon to appear as they do in a particular game, this is your chance. It applies to the whole team, so you can't have one pokemon with colloseum graphics and one with Emerald Graphics(at least to my knowledge).
2-Also on that screen you will see tabs with PKMN and then the pokemon party number right after it. By clicking that tab you can edit what pokemon will be in that slot.
3-In the PKMN(pokemon slot number) screen you see an array of info and choices.
- The Pokemon Field- This is a drop down list that lets you pick the pokemon you want added there. You can also just type in the name and hit the enter key. As you will see it will try to show a possible autofill as a suggestion. Using a letter key is also a quick way to go through the list if you happen to know only the poke's name's first letter.
- Below the Pokemon field you got the nickname field. This gives a name to your pokemon.
- Below the nickname field is the Held Item field. It works much like the Pokemon field except for items.
- Below the Item Field you got a list of all the moves it can legally learn. Just check the move you want it to have. If you decide you want to get rid of the move. uncheck it. No big deal.
- You have probably noticed that next to the Nickname field is an 'Expert' Button This allows you to chose whether or not it is shiny, pick its trait, pick its gender, choose it's hidden power type, to change your IV's, and to change your EV's. Also in the Expert window you can change your level. Default(and what much of the server plays at often) is level 100. You can change it as you wish.
- Also in the PKMN window are some buttons on the bottom of the screen. You can access boxes just like in the games, you can save or load teams, or you can rearrange the order by clicking arrange. This way you don't have to get rid of your pokemon in order to change your lineup order. There is also the done button which brings you back to the main screen.
4-Additional tools available are in the main menu.
4a-Under 'DataDex' you can access a variety of useful tools.
- The PokeDex- Just your average PokeDex that is searchable by various means, and that shows min and max stats at level 100. Quite useful for finding the one poke you need to complement your team.
- You got the MoveDex- It lists all of the attacks and gives you information on them. It also allows you to search for pokemon with the selected move. In addition it lists all the items and thier affects as well as the pokemon traits. It also alows you to search for pokemon with the selected trait.
- The BattleDex - Never leave home without. It gives a comprehensive chart showing what is supereffective against what and what resists or is immune to what. Very useful chart if you haven't memorized it already.
- The DamageCalc- Another never leave home without. It calculates the possible damage that you will do. Useful in battle and when building the team. Such as I made my machamp capable of surviving a full powerd psychic from Alakazam, leaving just enough health to fire a retalitory attack to kill alakazam. I would never have known how many ev's I needed off of the top of my head.
- When you open any of those windows the tabs on top will navigate between the four options.
4b- In the team builder there is also a version option on the main menu. This lets you pick which of the games you want to adhere to, or if you want to apply a server mod(such as smogon has a mod that implements the moves from the recent game(can't think of its name off the top of my head).
That should be enough to get you started.
I am on from time to time. But I have been sick as of late. And have been a bit... temperish.. Meaning I ain't really in the mood to play the guessing game invovled with pokemon.
Also as a note you have to have a full team before you can battle(or at least you did last I checked).
If this isn't enough, point me to what exactly you need help with and I can go in further detail there. I just didn't want to spend hours writing a post containing a detailed walkthrough.