Supply Depots are amongst the most important buildings in R.U.S.E. In most cases, your depots will be your primary source of income, at least in the early stages of just about any battle. Engineer trucks can only build depots on top of existing supply deposits, marked by yellow cubes on the map. (Zoomed in, the yellow deposits are revealed to be yards filled with oil drums).
Every 30 seconds, a convoy of three supply trucks will leave a Supply Depot, and travel by road to the nearest friendly Headquarters; either your main headquarters, any of the Secondary Headquarters you may have built, or even your allies' Headquarters (the supply trucks' route will be the shortest possible one, even if that means entering hostile territory). When each truck safely arrives, it adds $3 ($6 in Nuclear Mode) worth of resources to your total. This income is necessary, but remember that it is temporary and will not last forever. By all means defend them while they last, but placing heavy defences by them might not be ideal in the long run.