Starting pot question!

Alright. So I'm currently germinating some seeds and will be putting them into soil tonight, but have a question. I currently have a few seeds going and they are in styrofoam cups. However, I found some 2.5" circular clay pots the other day and would like to put the new seeds in there. The problem is that I want to have a constant pot size or canopy, so here's the question:

Should I put the new seeds in styrofoam cups as well or would it be okay to put them in the smaller clay pots (about half the height as the styrofoam cups). How long would it be before I"d need to transplant?

Thanks in advance. Any help is most welcome!