Each control you create in Condes is assigned an SI Unit number. If you already know which SI units are available for your event then put the lowest number in the dialogue box when you create the first control, and the number will increment for all following controls. 

The control numbers are passed from the Condes file to the SITiming event software so it understands the courses. When taping control sites in the bush, write the SI number on each tape to help ensure that each unit is at its intended site. I saw an Aus MTBO Champs organiser grieve when he realised that the last couple of controls he put out were switched, and the elite courses would have to be voided. 

If you start Condes work before knowing the SI numbers then you can renumber all controls in one go later. Renumbering all controls is irreversible, and obviously just wrong if some sites are already taped and numbered! However if needed it is achieved in the Control > Renumber Controls… menu. 

Auto-numbering by Condes skips those numbers which can be mistaken if read upside down. These include 66, 68, 86, 89, 98, 99. That is, Condes will allocate only 44 controls between 51 and 100. If you really need all 50 controls in that range you can manually renumber in Condes to fill the gaps. If you are so bold then make damn sure that 68 and 89, say, are not adjacent in the terrain.

To manually change control numbers, double-click on the control and overwrite the number in the Code box, top-left of dialogue box. [Actually I rarely double-click on controls because a shaky hand can bump the control off its location. Instead I click in the Edit Controls list on the left of screen, or if scrolling through many controls (tweaking control descriptions or circle cutting), I will use the ‘next’ arrow in the dialogue box. See red arrows below.]