NOTE:I'm assuming you understand the basics of the portable pokemon games. I will not tell you what a pokemon is, how battles work, or what moves do what.
Part 1:What is Netbattle
Netbattle is a pokemon battle simulator. It lets you pick your pokemon, their gender, their trait and nature, and modify their Ev's and Iv's! Then you can battle people online suing your team with the program. To dowload it, go here:
http://www.smogon.com/netbattle/downloadPart 2:Making a team
Now after you download and install the program, its time to make your team. On the opening screen, select Team Builder, then click on pokemon 1. The screen should look like this:

See that box I circled under pokemon, click on the arrow next to it, and a list of every pokemon in the game will come down. Select the one you want and it will be added to your team. In the second box I circled, you get to pick the Item to give to that pokemon. Then pick the moves your pokemon will have, and adjust it's nickname(if any) and your done for this sceen on this screen.
Part 3:Expert Screen
You see that button labeled expert on the previous screen? Click on it, because it's time to adjust the more advanced options of your pokemon. First off lets look at the expert screen real quick:

Here you can adjust a pokemons Ev's, the type of it's hidden power attack(if you're using it,)It's gender, it's trait, and it's nature. I won't tell you what does what, because it's all clearly labeled. Once you set everything to what you want move on to the next pokemon and do the same. Make sure to save your team when your done.
Part 4:Adjusting your player info

On this screen, you can adjust the usernae you will be playing under, the sprites you will be using in battles, the message that pops up after you/win lose, and any personal info you might want to add. Once again, I won't tell yu what does what, since it should be easy to figure out considering I'm letting you see what I put in each area.
Part 5:Picking a server to play on

On this list you will see of all the servers you can play on. Pick 1(I reccomend smogon university, at least while your just starting.) Aftethat a screen will come up with everyone else on that server, a list of serven info, and a box that lets you chat with other members. Now you can wait until someone challenges you, or you can challenge someone yourelf. You can pick the rules for the match that way. After you/your opponent accept the challenge. Now it will play like a normal pokemon battle. Have fun.
If you have any more questions, pm me about it.