The best case is to MLB the shop CEs - the spawn bonus maxes out at 100%, so you can get the whole bonus with one CE slot. Past that, use as many drop bonuses as you can. If you don't have it MLB yet, drop bonuses are probably a better value for the slot until you have a bonus of +3 or greater. Make sure you're using the right CEs for the mission! Bringing a +copper CE to a mission that only drops silver is a waste.