I realized pretty early on that I would need access to the track inside of the tunnels, if at all possible.  The ceiling tile actually lent itself well to creating access hatches that would fit right into place.  As I built up the layers, I cut the portions that would comprise of the hatch, and then glued the layers of the hatch, just like the other layers.  I sanded down the hatch and opening so that things fit well, and in some places, I added wood filler to fill in some gaps.  I used wood filler in this situation because it is much more capable of standing up to constant use than spackling compound.  I sanded down the hills with the hatches in place, so that everything lined up properly.  In the picture below, you can see the hatch removed, and sitting next to it's opening, right after sanding (you can see some of the dust from the sanding under the hatch).
Once the hills and hatches had been covered with spackling compound, they were given ground cover at the same time as the rest of the layout.  Once that was dry on the hatches, I made two holes through each hatch.  I made six trees (two per hatch) out of 10 ga. wire, which was thicker than the other trees on the layout (see TREES under SCENERY for more information on how I make some of my trees).  I left the trunks very long, so that when they were installed in the hatches, they stuck through the hatch, and at least two inches  beyond the bottom.  The pictures below show the junction hill access hatch with the two trees being installed.  First, the trees were installed to their proper depth, and temporarily held in place on top with clothespins.  I then flipped the hatch over, and bent out the bottom of the trees at the right height.  I then removed the clothespins from the top, and clipped the "roots" of the trees on the bottom with clothespins, so that they were held away from the hatch.  Any excess wire is clipped off so that it does not interfere with the way that the hatch sits in it's opening (the picture below left shows one tree at this point).
After all of the soldering has been completed, the trees are returned to the proper height and held in place with clothespins on top.  The hatch is kept upside down, and copious amounts of full strength white glue are used to glue the roots to the bottom of the hatch, and allowed to seep down the hole to adhere the tree trunk to the hole itself.  The full-strength glue seeps slowly into the hole, so I would come back every hour to fill it up, until it wouldn't seep any further.  The picture to the right shows the hatch after trees have been installed, and the glue has dried.
 
The reason why I've built these trees with thicker wire, and attach them to the hatch so securely, is because I can use them as handles for removing the hatches.  I simply grasp each tree at the trunk with my thumb and forefinger, and lift the hatch out (or replace it).  This way, there are no visible handles, and the hatch does not need to be pried out with a screwdriver or other tool.
In the picture above, you see the opening with the hatch removed, and a high-cube box car illustrating the narrowness of the tunnel.  The picture below shows the completed hatch in place.  The seams are still visible now, but will be camouflaged with foliage when this hill is scenicked.  More information on the construction of the hatches can be found in the MINE ACCESS HATCH and HILL ACCESS HATCH pages.
I then soldered the roots around the clothespins (which kept the heat away from the ceiling tile, which breaks down under soldering gun heat), which ties the strands together, and significantly stiffens the roots at the bend.  Once cooled, the first tree is returned to it's proper height, and the second tree is set up for soldering (the picture below right shows the other tree at this point).