I dunno if I've ever played Nautilus with the Ikes but you want to get a really good leash at blue and even a harder one if you dare start red. You can't do wolves/wraithes without help either cause Naut's clear is way to low without a level 2 shield. So when you hit level 3, first deduce if you can gank someone if not do not get dredge line and farm straight to level 4. I find farming straight to level 4 to be most effective.
You'll want a FH as you love all the stats, especially if you are giving blue buff away. Wits end is also amazing as your shield scales of attack speed with the more hits you can do with it up. Boots of mobility really help with ganks, but if the other team has a lot of CC, you'll want mercs. Get a HoG or philo, (or both if you get ahead, Naut's ganks are pretty deadily so it happens) If you get a glacial shroud, your mana should be fine to clearing so you don't have to get a philo stone.
Runes are attack speed reds, armor yellows, MR blues, and movement speed quints. If you don't have movement speed use AP quints as Naut scales off AP. Masteries i'd say go 0/21/9 for longer buffs and faster movement speed (or mana regen)