If the enemy team builds MR you just go right through it with your 50 magic penetration plus void staff. With this build you play ekko more as an assassin than a team fighter, you just dont have the health to tank some early shots before the fight so instead you just murder their ADC with a lich bane empowered E auto, early laning will be a bit difficult until you get your lich bane and sorcerers boots, and if you get ganked you dont have much health to really figt which forces you to either ult and try to get out, or run and hope for the best. Without a zhonya's you're screwed if you get caugt out. But like the assassin you are, you will be doing true damage to the their ad carry, unless they get an edge of night or abyssal to counter you

Its actually very simple, throw a Q and hope to hit them twice, if you hit once against ranged champs just wait for it to be off cooldown and try again, if its a melee however, when they try to CS smack them once for the second passive stack then E lich bane auto them for tons of damage, throw a q and auto them once more and they are either dead or flashing away from you, but lets suppose you mess up and get close to dying what do you do, well just click R and try again, ekko's ult has a fairly low cooldown that it doesn't really matter that you only have 30% CDR because his ult is up every 40 seconds or so at max level.