They might be too shallow.

Try a dollar store and get the lasagna pans with the clear plastic lids. That is about 6" of height. With 3" of soil, you should have plenty of room.

Thanks for the tip greengardener! :) The only thing is, I like the idea of having separated cells for each flower. I want to be able to sow a variety of things in close proximity to each-other without them getting mixed together.
Hmm, maybe I could use your idea of the lasagna pans and then buy those peat pot things to put in them. That's a thought!

Use cardboard or even aluminum foil to seperate within the pan?

I know peat pots dry out real quick, so if you can make sure the peat pots are in the soil in the pan, it might not matter. But keep an eye for dryness more often if you do use peat pots.

The shallowness of the pans is definitely going to be an issue, and will likely cause you more work in the long run.
A better option might be to use the trays simply as 'holding corrals' for a deeper container, such as styrofoam cups or other cups, or even as bottom-watering bins. You'll need the depth of soil to keep the containers from drying out.

I have a trick that works great for peat pots:
Take a few layers of newspaper or paper towel and line the bottom of the container you have the peat pots in, bottom water and use as a wicking mat.
I hated peat pots until I came up with this, I tried the one year sinking peat pots in soil in a container to Ws, but I found the wicking mat worked much better