Chit assignment in Catan: Seafarers, Scenario 8: The Wonders of Catan?
It looks like you're mixing two things up.

The Chits in this scenario are not the same chits as the victory points ones.
I don't have the material at hand, but you could use something completely different for those chits (a coin for instance). It's just used to track your progress in the wonder you're building.

The first time you pay the resources to build a wonder, you take the corresponding card for that wonder, place it in front of you as it is now yours (nobody else can build it from now on) and place your chit in the first step on the card. When you pay the resources a second time, you just move your chit to the second step on the card and so on until you build the fourth step.

This chit is not worth a victory point. If a player builds the fourth step of his/her wonder, he/she wins and that's it...
The victory points are used for the alternative victory condition: You win if you have 10 points and you're ahead of all other players on the building of your wonder.

More over, in the rules for this scenario, the chits are listed as "Additional Components" which tend to prove that they're not a part of the included game material (hence not the victory tokens).

Hope this helps...