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The potions are optional just depending on whether or not you want you boots faster.
Boots
Spellbook
Healing Potion
Mana Potion
Shoes of Focus
Book of Thoth
Chronos' Pendant
Spear of Desolation
Stone of Fal
Mantle of Discord
Bancroft's Talon
Polynomicon
Obsidian Shard
Soul Reaver
Divine Ruin
Ethereal Staff
Rod of Tahuti
Aegis first Unless they have someone that can pull like Da ji/ Ares then Purification Beads.
Aegis Amulet
Purification Beads
Blink Rune
Shoes of Focus
Book of Thoth
Chronos' Pendant
Spear of Desolation
Polynomicon
Rod of Tahuti
Shoes of Focus
Book of Thoth
Chronos' Pendant
Stone of Fal
Bancroft's Talon
Obsidian Shard
Y
B
A
X
This is my first guide so I thought I should start with the God I play the most. I am no expert at the game but I know with a good set up in the arena that this build packs a punch and can definitely land you a penta kill. But I will say this won't stand up very well in conquest as its based around pumping out as much damage as possible and securing kills.
The skill point order for Scylla is pretty straight forward you max out each ability before moving to the next one starting with Crush. This is due to Scylla's passive 
Quick Learner which gives 25 Magical power for each ability max out. Also Scylla's abilities have extra effects when they reach max level such as Sic 'Em which will root 3 enemies in range instead of just 1. At level 8 you should point skip keeping your 2 points for level 9 where you can put one in Crush and one in I'm a Monster.
The reason I personally take Shoes of Focus over 
Shoes of the Magi is because CDR in arena is key (for Scylla anyway) having max cool down reduction on 
Scylla is a must regardless of what else you take with her and the shoes are a good start to helping that plus they stack well with Book of Thoth. Following that up with Book of Thoth give you a scaling magic point boost as the game goes on. Follow this up with Chronos Pendant as it will provide heavy Cool down reduction which will help you follow up you Sic'em Crush combo more frequently and provide more chances to secure kills
For the 4th item I usually go Spear of Desolation unless i'm being 1 shot by mages or assassinated by Loki then I go for Stone of Fal. Mantle of Discord is only really there for if you are being focused none stop.
The 5th Item choice is life steal as following up continuous kills with I'm a Monster tends to leave you low on health or dead if they can kill you before you can chain kill so getting some life back from each kill is essential.
The last item is pretty self explanatory and just depends on what you are fighting. Heavy defences Obsidian Shard. Strong heals Divine Ruin etc there is not much more to say about this slot other than it is the interchangeable one however if you are close to magic power cap i'd recommend that you make yourself a bit more tanky with this slot so that its safer for you to ult and get out if needed.
Relic choice in this is pretty straight forward Aegis Amulet first unless they have someone who is going to pull you in like 
Da Ji or 
Ares then go purification beads followed up by Aegis Amulet
For Scylla's Early game you want to go and pick up the mana camp unless you have a mana hungry support like 
Hel then go for the damage camp. Once you have that leave your team to finish the camp/s and head straight to the mid to clear minion wave as best you can (keep distance if other team have come out early). This is due to not taking sentinel in the start talent choice so the faster you get this level the better (as escape is vital). Using I'm a Monster Early game isn't the main priority for kill securing unless you have someone like Ares who is going to set them up for you or your team is mostly melee in which case you will be cleaning up for them with it.
I'm a Monster at the right time is essential for setting up her multi kills and should be used when 1-2 are about half health so that your ult is reset and can be pulled off again. Don't be afraid of aiming for someone who have just manage to escape into the enemy fountain if they were very low as most people don't expect two dogs to peer over the wall and finish them off for lunch. Chasing someone down if sentinel is not enough is also justifiable just make sure that there are no other enemy gods coming to assist.|
Pros:
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Cons:
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All in all Scylla is a great god and really fun to play. With a few good set ups and maybe a little help from the team she can easily wipe the enemy team out without much hassle. But anyways I hope you liked my first guide and I hope that it has helped at least someone enjoy themselves in arena because that is what games are for at the end of the day enjoying our selves. Also please leave some constructive feedback on what I could improve with how I presented the guide and what I could have done better as I am planning on making more.
Major Update to item order (now in a more efficient order)
Changes to Item Chapter to fit appropriately with the new order
Added Extra Chapter Explaining Skill choice
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You should point-skip. It's difficult to state it in your skill order, but what you do is don't put a point into anything at level 8. At level 9, you'll have 2 points to put into skills, at which point, you can put the last point into
Plus I won't recommend you do double stacking on Arena, 'cause usually you won't farm minions enough.
Also considerate do some more penetration such as
Also if you're not building
For example, I see you like to get
Also your levelling order seems a bit odd, you seem to delay points in your ultimate and it only has 4 points allocated to it.
Going back to base often means you miss out on one minion wave, depending on timing. 50 gold per potion (I'm only really talking about getting a couple at the start) sets you back almost nothing, but allows you enough mana to stay out for at least one or two waves more, which is not only gold but early XP as well. That early XP could be the difference between me hitting level 5 before enemies at level 4 that might have backed once already.
You want to always have enough mana to be able to engage with your kit if the opportunity arises. Could mean the difference between you getting a kill (or you not running out of mana and not being able to use an escape if things turn bad).
(Unless I'm a hunter, I don't often get starter items that might have a bit of MP5 in Arena)
Also, keep in mind, early game, 60 mana for a level 1 ability takes a good chunk of your mana pool (13% if I'm
That's worth a bit of gold to me. But of course, that's my own preference. I don't care how anyone builds if it works for them...this one gives me a bit of comfort.