Actually it maked more sense to use the vehicles heating system while driving. The answer from TRUMA is:

Yes. With Combi and Trumatic E heaters, the heating function can be used without a problem whilst driving. 

In the case of Truma S / Trumatic S heaters, however, the heating function can only be used together with a cowl top, which must be installed freely in the air flow. Truma recommends cowl top T3 or T2. Otherwise, the flame may burn back and cause damage to the heater. 

Additionally, the cowl top must protrude at least 10 cm beyond any additional roof accessories (roof boxes, ski racks, luggage racks, etc.) so that the heater can function without problems.