PokeGen automatically fills in the hidden hex values and trashbytes for you. Aside from the obvious things (like your met at stuff, your PokeBall, your Ability, etc.), you just need to worry about the PID and your EVs.
You want to make sure that your PID was generated with the correct algorithm. Here are the 4 most common algorithms, and the Pokemon that use them:
Spoiler!
To generate a valid PID, click the F button, then select the correct algorithm, the Nature you want, and the IVs that you want, then press "search". It may take several minutes to generate your PID, depending on whether or not you wanted your Pokemon to be Shiny, and whether or not you wanted it to have flawless (or close to flawless) IVs.
When distributing EVs to your Pokemon, you must not exceed the internal limits of the game. Your Pokemon's EVs must not exceed 255 per stat. The total sum of EVs for all the stats combined must not exceed 510.
If you have any other questions, or if I haven't listed the algorithm that you wanted, then let me know. If this is your first time using PokeGen, then go ahead and post a few Pokemon that you have made. I will show you how to correct your mistakes.