|Sounds to me like it's working great, so I'd stick with it. It's normal for the diaper to be pretty saturated in the morning. If it's completely saturated, I definitely wouldn't remove a liner. When my son was that age, I used a bamboo OS with bamboo liner and a cotton liner with stay-dry barrier, so pretty much the same you're using, but it wasn't enough and I started having leaks. We thought an extra liner would make it too bulky, so someone suggested adding an extra liner outside (on top of) the diaper. I can fold it in two and put it where my son needs it most, and the cover holds it in place without any problem. It saved the day for us.
Now that my boy is older, we usually manage to get him to use the potty at bed time and we can then skip the third liner. But it's something to keep in mind if you ever need it... Some parents hate to change a diaper that is completely saturated and just want that extra bit of absorbency.