xplorer² by default remembers how it was the last time you used it, and when you restart it next time, it should appear exactly as you left it. That goes for almost all properties like the size and the position of the window, toolbars, pane arrangement, view styles, bookmarks and user commands, color coding etc. As long as you leave the default option Save program state on exit enabled, you won't experience any problems.
The default location for xplorer² settings is the windows registry (the ultimate version can also use a settings file for portability).
Occasionally there are users that have problems with settings. xplorer² seems to develop alzheimer's disease and forget about some settings. This is especially so for view-related properties like the on/off state of color coding, the column set for the detailed view mode and so on. What happens? The problem with a complex system like xplorer² is that there are many different configurations so there are many ways things can go wrong. If you have problems with your settings please go through the following checklist:
ps. From version 4.0+ tabs can remember their different settings even after a restart
This list should cover most settings problems — imaginative users may find other unintended ways to knock things off kilter <g>.