Let me answer a somewhat more general question. If what you are stacking are real hats (they have an ID EEPROM), yes. If both hats are using the same bus, say, I2C or SPI, a good designer would either have provided little short/break pads to change the I2C address, or alternate CS pins.
in your case, one of the components is a simple breakout, not a hat, so it's up to you to decide how to connect it. Here are some bits of advice:
Use a stacking header for the motor hat (and be careful not to solder it the wrong way up -- not that I know about such things :) ). Then you have pins sticking out which are a lot more convenient to connect to.
Use standoffs to keep the hat firmly attached to your Pi.
Ordinary GPIO pins on the Pi are NOT 5V tolerant, but the Rx/Tx may be (I don't remember off hand, as I already use a 3.3V FTDI cable) -- if the fona uses 5V logic, either verify that the Pi can tolerate 5V on Rx, or use a level converter.
- The fona board has an RTS pin, which you may or may not be able to disable on the fona side. I believe there is a way to expose additional UART pins as alt selections on the Pi, but I can't find a reference right now to include. It may be better for everyone involved if you just spend an extra $15 and get an FTDI friend to connect the fona instead of relying on the Pi uart. This will also solve your 3v3/5v problem.
Adding to @recantha's comment, if you switch to an Pi3 at some point, the tty device will no longer be /dev/ttyAMA0.