Your doing it wrong, NO, the way your doing it, it's wrong.
You should not be customizing your rune pages per champ, there are over one hundred champions, and I sincerly doubt you have the time or the inclination to buy over one hundred rune pages and customize them for each champion.
Furthermore that would be even more complicated than it initially seems, as many champions can fulfill multiple roles which means they would need a different rune page for each role.
Rather, I would do as is suggested in the linked question, and make general purpose rune pages for the different ROLES in the game, and apply the appropriate page to whatever niche your champion is going to fill in the game.
Some thoughts on to the roles:
Is your champion goin to be Offensive (Damage dealer), Defensive (Tank), or a balance of the two?
Does your champion focus on Attack Damage or Ability power to deal damage? (Or is your champion a hybrid?)
Is the enemy team heavy on AD or AP? Because of this, should your defense be focused on Armor or Magic Resist?
Are you jungling?
Does your champion have something special about him\her that calls for a unique rune page? (IE: lots of people swear that Move Speed Quints are mandatory for Skarner)
It's important to note that while some Mastery and Rune choices are no brainers, many are not. And what works for someone else might not neccesarily work for you. In the end it's a matter of personal preference above all else. Take what works for you, and experiment often to find new strategies and ideas.
Final Note: You should NEVER buy anything but Tier 3 runes, as any runes bought during Tier 1 or 2 will simply be phased out when you can purchase Tier 3 runes. Best to save your IP until your level 20 instead of wasting it on runes your eventually going to discard anyway.
This question may offer some help as well.