The Magos, I'd say build how you think looks cool. But I personally go for the Macro Stubber and Volkite simply because that loadout forces many wounds with decent strength.
The Onager doesn't have one option that is objectively better than all the others now. The Neutron Laser is great for heavy vehicles and monsters, the Phosphor weapon is good for light vehicles and heavy infantry, and the Icarus Array is doom to flyers and skimmers.
For the Skitarii Infantry, I recommend you play the long game and assemble them in a less than ideal fashion now, to then have a better setup once you manage to get your hands on a second box. I recommend building four Rangers. One leader, one Transuranic Arquebus, and two scrubs. This way once you have a second box you can have a unit of five with two Arquebii without having an extra Ranger that doesn't fit in being left over. Then the rest build as Vanguard. I recommend you build both the special weapons, as both are useful. The Alpha's melee weapons I generally don't bother too much with - he's just not all that suited to combat - but you can use them if you like. The Phosphor Blast pistol is still a good choice in 8th by the looks of things, and the Arc Pistol compliments the Arc Rifle quite well as they both operate the same way. Again, once you have a second box you can have your Vanguard units equipped with two of each special weapon.
I've only played two games with my Skitarii in 8th edition, so take what I say with a bucket of salt.
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