I like to think of TransX as a layered Transfer MFD that will help calculate when/where burns should be done. Learn how to use Transfer MFD if you don't know already.
As always start with trying to read through the manual.
At each stage you change each variable one at a time. For instance to change the target, you use the VAR and VR- buttons to select target then use the ++ and -- to change that variable.
If you wanted to go from Earth Orbit to Phobos, you would start with the view showing your orbit around Earth, set the target to escape and hit FWD to get a Sun Centric view, there you select Mars as the target, hit FWD again and select Phobos as the target. Hit back until you go back to the Earth view and it will have a trajectory for you.
You need to play around with the variables to get the exact trajectory you want. Really, just boot it up and play around with it.