"then placing a flat plate on top...."
Then you're not making an open top mold.
When you pour your resin place the mold on a hard surface. Take an appliance that has some sort of vibration to it and place it on the table next to your mold. The vibration will help the air bubbles move to the surface and help the resin settle into all parts of the mold. "Laying" your resin initially into the mold will help with the bubble issue as it makes less bubbles. Also when you mix up the resin and hardner, go easy. You can make alot of bubbles just by doing that. Pouring makes bubbles simply by the physical action of trapping air as the liquid pours or as the resin covers the small voids of the mold. Open faced molds are easy to pour into by pouring down the sides of the mold and letting it creep along the surface or by gently brusing the resin on the surface and allowing it to fill all areas that way. Then you can top off by pouring if you like but again, pour along something and let it creep along the surface to fill the mold.
Ideally if its a large project or you are going to be doing alot of resin casting, I'd invest or build a vacum table and that will just about eliminate any bubbles.
A simple, slight over pour and let the resin sit proud of your mold by the action of suface tension will serve the purpose and sanding the excess off works great.
Mike
"Imagination is the dye that colors our lives"
Marcus Aurellius
A good friend will come and bail you out of jail...but, a true friend will be sitting next to you saying, "Damn...that was fun!"