Speakers on top of subwoofer

This is not a problem. Simply use a vibration isolation pad/feet between the speakers and the subwoofer. 

Think for a minute how many expensive large floor standing speakers have large, vibrating bass drivers in them. Too many to count AND they have no way to eliminate bass energy going throughout the speaker and crossover since they are connected to the same cabinet as one unit.

One other big advantage is the subs would be positioned properly for stereo image especially if using higher crossover levels. ( Subs set with slightly higher crossover can be locally identified)

You also gain an advantage to isolate the two cabinets in your set up  and still properly aligned. Highly recommended.

@soix  

+1 no speakers in top of subs. Also, for optimal sound you will have to move them around… optimal can be almost anywhere in the room. 

@ghdprentice    Don't do this? Wilson is doing it wrong?  BTW...these go down to 20 HZ.   B&W, TAD and many others do the same split configuration.

@gdaddy1 +1

Mike

You're placing your speakers in the optimal position for your listening. That doesn't mean that is the optimal position for the subs. Sub placement will be trial and error until you find the optimal placement.