Owellow

There's some pretty good mapping info on the forum, I'll include links at the bottom. Mapping with systems like this has an easy learning curve if you put in the time. It's all about getting in there and tinkering. Anywho, I'll answer one of your questions, and then briefly explain layers.
 
Invisible barriers are simple, you just click the Attributes tab in the editor, select 'Blocked', and place the square wherever you don't want PCs to go. There's other ways to do this, but this is the simplest. 
 
Mapping layers work like this: 
 
Ground layer is your foundation. Usually no transparency in the source images. Grass, dirt, water, etc.. 
You then build up from there, using Mask 1 for details, some people put buildings (or parts of buildings) in this layer, tree bases and trunks, other tall object bases, flowers, rocks, etc. 
Mask 2 is detail on top of detail... stick some mold on that rock. 
Fringe 1 and 2 work the same way, but the PC will appear BEHIND non-transparent objects in this layer. e.g. tops of trees, center of bridges, tops of signs and fences, etc. 
 
If you put the time in... mapping, to me at least, is the simplest and least daunting obstacle to tackle when creating something from the ground up. I see this is your first post.. which makes sense that this is what you're most concerned about. Be sure to check out the guides and feel free to shoot me a message with any questions. 
 
I've included some links to things you may find useful. 
 
peace and good luck. 
 
 

Ah! Set to Cliff..... Thank you. derp. So, for roofs, walls, cliff walls, etc... set Tile Type to "Cliff", in case anyone is a nub like me. 
 
peace.