The Window submenu allows you to change perspectives as well as to use your own perspectives. The FXML source code for the default perspective can be found in the ProB2-UI Git repository. You can modify a copy of this FXML file and load it as a custom perspective.
Every component may be placed as you see fit, but to guarantee certain usability, you need to follow through these rules: Every detachable component needs to be placed in a TitledPane and these TitledPanes need to be put in an Accordion and each of these Accordions need to be registered in a list as shown at the end of the FXML file linked above.