Arcane Comet is a great keystone choice for Vel'koz as it reliably empowers his ability to poke in lane. Thanks to the slow from [Q] and [R], and the small knockup from [E], you should be able to reliably land Comet if you are hitting your abilities.
WhyThe Ultimate Hat
With your [R] up on Vel'Koz you can constantly threaten the potential of a 100-0 one-shot if you're able to land a full combo. More [R] uptime means more outright damage threat.
Transcendence allows you to hit 35% CDR with just Morello's and Cosmic Insight, allows you to spam your abilities for poke damage and kill pressure.
Scorch further empowers your ability to poke and harass in the laning phase. If you're able to proc Scorch on cooldown several times before hitting level 6, you should be able to keep your lane opponent in kill range when you skill [R].
Magical Footwear is a great rune choice on just about any champion largely for its raw gold value with no input. Think of it as effectively gaining a kill's worth of gold at 10min.
Cosmic Insight is an all-around great rune choice on any champion, especially poke champions who are constantly looking to deal damage from range when their abilities come off cooldown.