I'm about to run the Storm King's Thunder book for two players. One experienced, one really not. I planned on giving the two a "personal body guard" that they can command but I control to balance the party a bit. Any suggestions for me or for me to give them?

One or both will learn Giant. One will probably learn Draconic. The experienced one tends to build brokenly effective characters so I'm not worried about him. But I've only glanced through the book so far, so are there any skills, tools, abilities I should warn or lean them towards? Lockpicking? Stealth? History? Cartography?

Also, I'm all for milestones, any arguments for using XP instead?

I haven't ran or played in SKT but from personal experience from just playing, let them play how they want.  You'll probably have to curve the encounters to their level.  To balance out the party, you could always have them each play 2 characters, but that is up to you.  Trying to guide them towards certain skills and abilities is a form of metagaming, since they know that they'll need this skill or ability but their character would not.  Personally, I'd say just let them make their characters how they want and see how things go.  That is how a lot of games are played as far as I know, and I think would be the most fun for them.  I'm a big fan of milestone leveling due to the simplicity of it and then you don't have to worry about keeping track of XP.  

This is just my opinion on the matter but I hope it helps.

This could be an opportunity to try out the UA sidekicks, or just make a couple of characters that would compliment some of their weaknesses. A bard or paladin could serve as face while providing support with heals, buffs, debuffs, and/or being a meatshield.

Wizard, bard, UA artificer, and rogue would have strong options for filling in skills along with the Expert sidekick.

It's been a minute since I looked through SKT, but I recall there being a lot of water areas at least towards the end. If they don't have waterbreathing, swimming speeds, or similar abilities, you can populate magic items to help compensate. 

I'd let them have 2 PC's each.

Thanks, the waterbreathing heads up let's me steer them or build some extra magic gear in. I planned on giving them two Warforged companions who will be designed to complement the party with the players making the actual decisions. They'll probably get a utility Wizard or Rogue as one of the "body guards."

And while my experienced player could probably handle two PC's without trouble, the new player is going to have a hard enough time role-playing and remembering what he can do with just one character. The theory is giving each of them a bodyguard/sidekick who'll follow their commands but they don't have to worry about.

I'm currently running HotDQ with 2 players - namely, my two kids. We had started with one character each, a Dragonborn Cleric of Bahamut, an Elf Rogue, and me the human meat shield Paladin. :) we hit the Kobold camp, and they went into full panic mode, freaking out about the number of kobolds & cultists, adn wanting more firepower. So i decided, what the heck. Now we have a Dwarven Fighter, a Gnome Wizard, and a half-elf Ranger as well... 

From my standpoint, things seem to be going well. everyone is having a good time, and the extra characters don't seem to hinder things.

But they both have been working with D&D mechanics for a while before we started playing, so it was easier for them to adapt to two characters. In fact, my daughter plays her gnome wizard with a British accent so we can distinguish which character she's using in RP scenarios. 

You could start the new player with one character & a warforged bodyguard, and as they get comfortable with the system, you could hand over control of the bodyguard to them.