If you're using fresh tomatoes, you'll want to blanch them and then remove the skins, then scoop out the seeds and pulpy stuff.
The next part depends on how you like your tomatoes:
Traditionally, you just crush them with your hands
you could give them a rough chop or dice
You could toss them in your blender for a very quick blitz.
The more you process your tomatoes, the more you may need to drain the excess water out of them. Lightly salting the tomatoes will also help the water to drain out.
After you've prepped your tomatoes, TASTE THEM. Since you're using an uncooked sauce, your tomatoes will sweeten a little bit while they bake, but they will taste like you want your sauce to taste BEFORE you bake. If they need a little sugar, now is the time to add it.
I prefer to used canned crushed tomatoes (muir glen crushed with basil is my current favorite), because there is much less prep time involved, and if you find a brand of canned tomatoes that you like, the flavor should be pretty consistent from can to can.
Good luck! Let us know how it goes, and please post pics when you can!