xtrkcad.ckp
are the check-point files created periodically while running XTrkCad. If your system XTrkCad hangs or crashes you get the choice of loading the checkpoint file and so recover (most of) your work by saving it to your current layout file.
The check-point frequency is set by the Check Point field found in the Preferences dialog (Options>Preferences).
xtrkcad.cus
file contains parameter information. This is mostly information created by the Turnout Designer dialogs (Section 2.9.8) and Group (Section 2.9.3) command. You can use the Edit>Custom Management dialog to manipulate these parameters.
xtrkcad.ini
(on MS-Windows) or the xtrkcad.rc
(on Linux) file contains various parameter settings from each use of XTrkCad. Most changes you make (such as scale, room size, window position) are saved in this file for the next time you use XTrkCad.