If you mean the way the handheld games do it, then sadly, no. Its a limitation of the starter kit. The pokedex version depends on the region of the map, and when you return to previous areas the pokedex will also revert.
Edit: For now, I'm going assign the Topaz pokemon numbers starting with 387. This can be changed later by adding in regional pokedex numbers, which won't affect any of the other programming.