You can use the Farm Designer to select the location of plants in your garden, and then import those locations when instructing FarmBot how to move in sequences. Anything that you would like FarmBot to do needs to be included in a sequence. For more information and example sequences, see the Sequences documentation. We are working on features to reduce the need for creating as many sequences, see this post about a recent software update for more information.
Your question about tool changes may be more appropriate for a new topic, but how are you dismounting the tools? The dismounting process should be the same as the mounting process, but in reverse. The z-axis leadscrew has more than enough strength to pull the UTM off of the tool after the tool is in the toolbay.