Merge visible ?

I have a question 'cause I do not understand this, nor my teacher (school's ps classes) and I hope someone can tell me the answer.

In this image there are tons of flaws and the job is to make it look great. The thing is, that after every fix the int. says you have to merge visible layers so obviously it flattens the image. But, at the end you have to have all the layers available and so you can edit them later on. I have tried to click off the eye option on some of the layers, but after merging and trying to turn it back on, the effects are suddenly gone even if I move them on top of the merged shot.

So what on the Earth I have to do so I can merge visible without getting the picture only on one layer ?