Don't know if this tip is elsewhere, but I have noticed that if you Cut an object or group of objects, and then paste, they default to being pasted in the same location they were in. So, if you hide all layers but the one you want to merge from, and do a select all (shift select) and do a Cut and then go to the layer you want to merge into, and then do a Paste, the objects should paste in pretty well.
I also use this trick to cut and paste an object to pull it to the top of the instance list -- (which effects draw order, (IN THE VERSION I USE (I actually haven't updated in awhile because newer version totally ignore instance create order for draw order and it totally breaks the way I create my levels in the room editor and I don't want to / feel like implementing the z-order stuff people talk about here) ) )