1) Make sure you use a PID that corresponds to your Pokemon's IV's, gender, shininess etc. Pokegen is really bad at doing that, so maybe try RNG'ing.
2) If you want to get the Pokemon to level 100, type in Level 99 if the Pokemon evolves twice, and Level 100 if it evolves once or no times. Then, if it evolves at all, lower the EXP by 1 point.
3) Raise EV's to desired levels, but not past a 510 total. Usual spreads are 252/252/6.
4) Give Pokemon desired legal moves and put 3 PP-Up's on (except if using Trump Card).
5) Save the file.
6) Go into game and level up once (i.e. evolve).
7) Save the game.
8) Go back into Pokegen and raise the Pokemon's level to 100. If the Pokemon evolves again, lower the EXP by one.
9) Save the file.
10) Evolve the Pokemon again.
11) Save the game.
Generally, dealing with nicknames is bad (due to trash bytes), so I start with an RNG'd base and NEVER nickname Pokemon.
Also, remember that changing the OT, ID, or SID of a Shiny Pokemon will invalidate the PID and make the Pokemon un-Shiny!
EDIT:
Check the pokemon you are trying to hack with
http://bulbapedia.bulbagarden.net/. All I know is that if it's a bad hack, pokemon battle revoultion will show it as a bad egg but it hasn't happened yet.
Also you probably forgot to click ok on the edit page.
Not always. I have had some hacks with everything legit but the PID show up as Bad Eggs, but then I've had a blatantly hacked Shiny Mew (Sacred Fire, Sheer Cold, invalid PID, etc.) come up as legit.