Your extra deck doesn't really matter here. Put whatever you want in the Extra Deck, as it's just fodder for Pot of Extravagance and Pot of Prosperity If you can, I recommend keeping Qliphort Genius in there, though, just in case you need to get more than one Qli back from the Extra Deck.
One of your most important cards here is Qliphort Scout. As long as it's in your Pendulum Zone, for the low price of 800 LP, you can search any Qli card from your Deck (except other copies of itself) once per turn. This is also a soft once per turn, so if you have two Scouts in your Pendulum Zones, you can do it twice per turn. Though I personally prefer only having one at a time out, in case your opponent has backrow destruction that hits more than one card, and the Pendulum Effects from other Qli cards can be somewhat helpful.
The Qli archetype encourages you to not Pendulum Summon (or rather Special Summon at all), funnily enough, despite being comprised almost entirely out of Pendulum Monsters. All but two of their Pendulum Monsters get decreased ATK if Special Summoned (or Normal Summoned without Tributing), and one of their two boss monsters, Apoqliphort Towers, decreases the ATK and DEF of Special Summoned monsters by 500. That's not that bad, though, since most of them give benefits if they're Tributed (Tribute Summoned for some), and being a Pendulum archetype, it's not too hard to get out Tribute fodder. It's not as easy as it was in MR3, though, and Qlis only have one Link monster to their name. Plus, every Qli Pendulum monster locks you out of Special Summoning non-Qlis if it's in the Pendulum Zone. Qlimate Change and Pot of Riches can help recycle Qli cards from the Extra Deck, but you can't rely on those too much, so you'll need make your Summons count. Your boss monsters are Apoqliphort Towers and Apoqliphort Skybase. Both Towers and Skybase are unaffected by Spell/Trap cards and activated monster effects from monsters with an original level lower than the respective Apoqliphort monster's current level (Towers is Level 10, and Skybase is 9), provided they were Normal Summoned/Set. Both of them require 3 Qli Tributes to Normal Summon/Set, and they can't be Special Summoned. Towers, as mentioned above, reduces the stats of Special Summoned monsters by 500. However, it also lets you make your opponent send a monster from their hand or field (they get to pick from where) to the GY. This effect is a soft once per turn. Skybase lets you target one of your opponent's monsters and take control of it until the End Phase. This is a soft once per turn, too.
Skill Drain negates the effects of monsters on the field, which will get rid of the ATK decrease on your Qli monsters from their own effects (the ATK decrease also won't return if Skill Drain is removed - the decrease from Towers will, though). If you want to get out Towers or Skybase, though, I'd recommend getting them out before you activate Skill Drain. Their effects will be negated if Skill Drain is up before they hit the field.