Change the size of the clone stamp so that it contains only your mountain ( [ and ] ) and make sure the Hardness is set to 100% (right-click and move the Hardness slider).
Alt-click in the center of your mountain. Since you're set to sample all layers, you'll get the black and grey of your normal brush, the white underlayer, and transparency around it.
Create a new layer to hold your mountains and change its blend mode to multiply. This will allow the background to show through, but the white will still mask out the mountains beneath!
For best results, you'll want to make several different variations of your mountains, but since they're all stored in that palette area to the side of your document, when you want to change to a different mountain, all you need to do is to alt-click the mountain you want to use, then stamp away.
The clone stamp can also be used to take bits from one image and stamp them into another, so if you want to keep all of your isometric mountains and trees in a single document that you use for every map you make, you can just keep that image open to one side and sample from it instead, saving you the time of prepping the palette inside your working doc.
edit: Remember to work from top to bottom when using isometric stamps. This will ensure that they layer properly.