Cross-sections are used in combination with plan or extended elevation, so you need to have section points *in plan and/or extended elevation scraps*. It's easy to insert section points in cross-section scrap itself. In this case, cross-section will not be displayed in final pdf output.
Go to “File commands control” panel, look for appropiate plan/extended scrap and click any line inside it. Then insert a point and set type to “section”. Xtherion will add new objects *over* clicked line, so don't click on “scrap” line itself or your point will not be in desired scrap. Anyway, don't worry if your point was inserted out of appropiate scrap, because you can click the line representing point section and move it with “Move up”, “Move down” and “Move to” buttons, until it's placed in the correct scrap. Also, be aware that cross-section will appear centered over this point in final pdf output, so please draw it accordingly.
After the section point is created in the corresponding plan/extended scrap, you need to give an option in options textbox:
-scrap <scrapname>
where <scrapname> is the name of scrap holding the cross-section. As you can guess, section point is calling cross-section scrap in order to get it drawed in final pdf output. You can place as many section points calling the same cross-section as you need (usually plan and extended elevation).