Please see the step by step installation video/tutorial for the KTM 690 auxiliary tank from RADE/GARAGE. Here are more details about this product: www.radegarage.com/parts/ktm-690-19-tank/
By putting the dust cover over the foam filter & fitting it to the airbox the way you did it would it allow dust into the engine as your not making a 100% sealing surface between the bottom of the foam filter & the air filter box because the dust cover is now the sealing surface & not the foam, the dust cover is not 100% smooth ,it has ridges & valleys it in, only small but enough for fine dust to pass. Correct me if i,m wrong , I think your surpost to fit the air-filter & cage to the airbox than put the dust cover over the fitted air filter