When you first turn it on, it's easy for the bubbles to climb all the way up the chamber and suck resin into your vacuum pump. That resin will harden inside your pump from the heat it generates and cause the pump to fail (unfortunately, I know from experience, lol). So if you can see inside the chamber, you can apply the vacuum gently and bleed off some of the vacuum as it starts, to slow the climb of the bubbles. I will say, one way to reduce those bubbles is by setting up your chamber such that you have an additional ball valve in your lid. This on/off valve is hooked up to another hose. With the valve off, you pull a vacuum on your chamber with only the piece of wood you want to stabilize and something weighing it down (no resin in it). Then you put additional hose in the bottom of your stabilizing resin container and open the valve. This sucks the resin into the chamber. It does seem to speed up the process a little to have the vaccum already pulled on the piece of wood and reduces the initial surge of bubbles.
But the main thing is to be able to see when the bubbles stop coming up from your piece of wood. That way you know when it's done. You can also just run it for a day and it should be fine, regardless.
In any case, just a clear lid will do just fine.