I'm working on multiple layers on Photoshop (CS6). Some of the layers have different layer styles like multiply. When I merge the layers together I seem to lose the transparency on some of the image, how can I sort this please?
It depends on what you're merging together. If you're going to merge the layers, I'm assuming you don't want to edit the layer later on.
Right-click the transparent layer, select Convert to Smart Object. Then right-click it again and select Rasterize Layer. Now you can merge this layer with others like usual.