Ok I have been able get multiple chunks to connect together and then go into game and wander around in them. I'll try the best I can to explain:
First off, this is kind of a combination of Asto's tutorial found here http://forums.runicgames.com/viewtopic.php?f=28&t=6791
and the tutorial found in the TorchED folder titled "Creating a room".
1) First I started with the Runic tutorial. Open the editor and click on view >> chunk palette. For my dungeon I opened CRYPT:1X1ENTRANCE_N. I applied this to the workspace. Basically what this does is give you a grid which will allow your player to exit this "chunk" northward to the next "chunk" in the level.
2) Next navigate to TorchED/media/layouts/crypt/1X1ENTRANCE_N folder (or whichever folder matches your orientation). I opened one of the chunks into the editor. (MAKE sure you add a player start point in this chunk)
3) Next I saved this "chunk" as its own layout (name it something you'll recognize. I named mine 1X1ENTRANCE_N_JS_A) in my mod folder. In My instance it looks like this mods/mymod/media/layouts/crypt/mymod. replace mymod with the name of your mod and crypt with whatever setup you decided on.
4) Now, I'm assuming you've read Asto's tutorial above, because there is some integration here. Read the part where he talks about editing chunks and such.
5) Open the dungeon editor and click on the rules tab. Click on the rules set you've made. If you haven't done so, make a rule set for your dungeon by copying an existing one or making a new one. Click on chunk types tab, and then click on modify under the box named "Chunk Types". click on the chunk type that matches the one you made earlier (see step 1). So in my case I click on 1X1ENTRANCE_N.
6) Next in the middle section click on the pull down tab under "folder". Navigate to where your layout chunk is saved from earlier (mymod folder or something like that). Then in the right hand box named "Inclusive Chunks". You should see 1X1ENTRANCE_N_JS_A (see step 3. Replace this with what you named it.) Click on it and add it.
7) This step is VERY Important. Click on layout. This is where you get a visual of how your chunks will match up. Right now all we have made is one chunk. It's a chunk that starts the player and exits him to the north. Now this confused me at first, but when you are looking at the layout grid here, SOUTH is ACTUALLY NORTH. And vice versa. I have no idea why. Anyway, keep that in mind. Right click on the center square and click on the chunk that says 1X1ENTRANCE_N (see steps 1 and 5).
8) Now you should see a little blue square with a red dot representing the exit out of this chunk. It will be on the bottom (which is the north side of the room as your playing). Now save this layout. If it gives you an error, exit out of the dungeon editor and reopen it. Readd the inclusive chunk from step 6. Now it should let you save.
9) Next, now that you have your first chunk it's time to add another chunk or room. Start with step 1 again. We're gonna make a new chunk. Only this time, we know that our exit from the previous chunk that we made is coming into the NEW chunk from the south (our first chunk exits to the north, remember?). So navigate to the chunk palette and find one that has south exit, it can be CRYPT:1X1SE or CRYPT: 1X1SW, or whatever, as long as it has a south exit to match up to the north exit from the first chunk. Apply the one you have chosen.
10) Next follow the steps from 2 on. When you open the new layout for this room (make sure it matches your orientation. For ex: if you chose CRYPT:1X1 SE make sure you chose the same layout. Use the coordinates on the right hand side if need be to make sure your exits match up with the yellow lines on the grid.
11) follow the steps all the way through including adding the chunks to your layout. As you add more rooms, your layout should match up. Meaning red squares (or doorways) matching up to adjacent rooms. Make sure to save your rules set often.
You should be able to load up the map and walk through multiple chunks now if you lined them up right. Hope this helps. I may have not been clear enough. I'll try to answer questions if you have any.