VH-FKI was tracking to Argyle via Fitzroy Crossing at Flight Level (FL) 250 and was approaching its descent point. VH-JJX had departed Kununurra, was on a climb to FL240 and was tracking via route T37. The aircrafts' tracks crossed to the west of Argyle creating the possibility for a traffic conflict. At the time of the potential conflict the duty Air Traffic Controller was working with the aircraft in his own sector (Sector 2) and supervising a trainee controller on another sector (Sector 1). The rated ATC from Sector 1 was absent on a short term break. Due to technical restrictions it was not possible to combine the Sector 1 & 2 consoles during this period (the normal method of covering a short term break). The controller, realising that the aircraft would probably be in conflict during their respective descent and climb, decided to calculate a minimum lateral separation point between the aircraft and issue VH-FKI with a clearance for its descent which, he believed, would maintain the minimum required separation. To calculate the lateral separation point the controller had to leave his console and draw a lateral separation diagram on the wall chart display. During this process he incorrectly used the Curtin to Argyle instead of the Fitzroy Crossing to Argyle track for VH-FKI. Consequently the minimum lateral separation point calculated by the controller was incorrect and the clearance issued to VH-FKI did not ensure the aircraft would be separated by the required minimum standard (1000 ft vertical separation at least 10 minutes prior to crossing). Fortunately, prior to commencing descent the pilot of VH-FKI checked the position of VH-JJX and delayed his descent until the aircraft had passed. Safety Action 1.The Civil Aviation Authority (CAA) will publish a lateral separation diagram for the tracks to alleviate the need to draw a diagram on the wall chart. 2.The CAA have taken action which will allow the Sector 1 and Sector 2 consoles to be combined should it be necessary.