I like to use the divide and conquer method. Since you are just starting
I would divide your Zephyr from the layout. If the Zephyr can run a
locomotive on a single piece of track you have a good start. Then the
problem(s) are on your layout. We found that the more isolated blocks
the better. On Jim's layout we have 5 major blocks, each with a shut off
switch. When we have trouble we shut blocks down until the trouble
clears. We are also limiting power routed tracks to those near the
frogs. This way a locomotive isn't trapped on track made dead by power
routing. A 12v. test light is a great aid to see if the power is where
it needs to be. ( cheap at Harbor Freight )
My layout has 10 blocks, I just created the 10th. I set a locomotive
with sound on the track I wanted to isolate. Then I cut the rails that
lead into the area. With those cut and the gaps filled with plastic I
started cutting wires under the layout until the locomotive shut down.
Then using the trouble light I reconnected the wire I shouldn't have
cut, and then gathered the rest to the new block power terminals.
Use lots of labels, make notes of how things are arranged. Take
pictures, have fun!