High efficiency furnaces will make condensate. They run the air back through the hot exhaust to get more heat out. This also cools your exhaust enough to use PVC - that's what your upper line is.
In the process of cooling the exhaust, you might get some condensation. Typically that's collected in a little sump tank. When the sump reaches a certain level, a little bitty pump pumps it out - that's your lower line.
If it freezes where you are, you might want to insulate that lower line. If it freezes shut, your sump could overflow in the mean time. It's just a dribble of water, but still. It's a leak of water in your attic.
You should be able to tell by the color, and connections used.
Gas
"Black pipe" is commonly used for natural gas, and is dark grey/black.
All connections will be threaded.
Water
Water lines come in a variety of materials, some of the most common are.
Copper
This will be um... copper, in color.
While there are other ways to join copper pipes, the most common is solder.
Galvanized
Galvanized pipes will be a light grey.
And use threaded connections similar to black pipe.
Plastics
You might also find various types of plastic-ish water pipes. These can come in a variety of colors. Red, blue, white, black, etc.
These may use compression type connections, crimp connections, or various other type or connectors.
Still can't decide?
Try using your other senses.
Touch the pipe.
If it's warm to the touch, it's likely hot water (may not be warm unless hot water was recently used). Hold the pipe and have a helper turn a nearby tap on/off quickly, to see if you can feel vibrations. Try running the water for a bit, then touch the pipe to see if the temperature changes. If the pipe gets colder/hotter, it's likely a water line.
Listen to the pipe.
Put your ear to the pipe, and again have a helper turn on a nearby tap. If you hear the water clearly in the pipe, you found yourself a water line. (make sure the pipe is not in contact with any other pipes when you do this, since sound could be transferred to the other pipe). This is not the most accurate method, but it can sometimes work.
Taste the pipe.
This won't help you at all. I just pictured people licking pipes in my head, and thought it was funny. You could tell your helper to do it, and then laugh at them when they do it. But it's not going to help you figure out what the pipe is.
Best Answer
There is nothing wrong with moving it to your suggested configuration. They probably went through the framing to make the entire configuration more secure. Make sure if you change it to make sure that you clamp it to the framing to make sure there isn't room for movement.