Hello!  I'm attempting to create a Wizard subclass based on named wizard's school.   As part of a subclass feature at 2nd level, I need to be able to grant them the ability to choose between 4 different skill proficiences (Arcana, History, Nature, or Religion).

I added a Modifier to the subclass feature, but I'm not sure if I'm supposed to choose "Proficiency" out of the Modifier types or "Choose Proficiency."   I'm assuming it's the latter, but it does not appear to give me a choice as to which skill proficiencies from which they can choose.   When I test it, all of them are open for choice.

Should I be choosing "Proficiency" instead and doing something else?   Is there something about "Choose Proficiency" that I'm missing?   Or is there another option altogether that I should be choosing?

This is likely not possible in a general sense.

Homebrewing subclasses on here is often unintuitive, so I usually start by looking at an existing subclass to see how it's implemented. Right now, only one subclass, the Knowledge Domain for Cleric, offers a choice between skill proficiencies. 

Unfortunately, this is implemented as its own modifier subtype: "Choose Knowledge Cleric Proficiency". If choosing between a specified subset of skills was possible in the character builder engine, this subtype would not be needed.

Fortunately for you, the Knowledge Cleric gets a choice between the exact same skill proficiencies you're using!

So, choose modifier type "Proficiency" (or "Twice Proficiency", as the Cleric gets, if you're feeling generous), then select "Choose Knowledge Cleric Proficiency" as the modifier subtype. Hopefully that works!

Funny I was just looking for a solution like this but I can't find the listing for "Choose Knowledge Cleric Proficiency". Perhaps because I don't own the content? But there was an option for Order Domain oddly, and I don't own that either.

EDIT: So far it seems you can make it like you would make a "Battle Master" fighter subclass. By giving the feature "options" and then specifying how many options at what level in the next line ("2" if only 1 choice at level 2) Then you need to list each option individually. When using that subclass at 2nd level, they should be able to make a choice but only from the options you listed (Arcana, History, Knowledge, Religion)

Huh. Knowledge Cleric is in the PHB, do you have access to that?

Using the "options" method is great, except for when you're already within an option (there doesn't seem to be a way to add sub-options inside options).
For example, I'm trying to recreate the UA Ranger's Canny feature under Deft Explorer, which gives an option between several skill proficiencies. Workaround (since I'm only using this HB for one character) is to just hard code the choice I was going to make.

I found this discussion because I'm basically looking to do the same thing except with a subrace.. I'm running into a problem though because for some strange reason, even though I own knowledge domain, I can only choose the proficiency set if I make a copy of that specific subclass. Is this just a weird bug, or am I missing something here?

Same, guessing this isn't something that's an easy fix :)

Same here, and I've noticed something else: Some sets that other races use aren't available unless you start with that race as a template. My example is that unless you start with the Changeling race, you can't access the Changeling Instincts choice set. And even then, if you remove it for something it, it vanishes from the options.

You can use Options to get close enough.

Each option is one of the skills you want them to be able to pick.

This might be a silly question, but could someone explain the Options feature in more detail? I'm working on my first attempt at homebrew in DND beyond, developing a Cleric subclass that has a similar first level ability to the knowledge domain cleric (just with different options). If I need to hard code the choices that a player makes offline, I can, but if there's a way to make the choice online, I'd prefer that.

Screenshots from a subclass I have that does something similar, grants choice of Deception, Persuasion, Intimidation, or Stealth

Top level skill:

 Level and options

 Options list

 An individual option

 The rest of that option

 Its modifier

This is amazing, thank you so much for taking the time to break it down for me! 

I run into the same problem with a homebrew race. My idea was simple, i wrote what can be choosen in the description. Then i created the profiency bonus with the choose a skill option and wrote under details to only pick from the options listed in the description. It is up for the DM and Players to do so and at least for a private game this could work (it does for my group) 

Please see the Homebrew Subclasses & Species FAQ #19: (https://www.dndbeyond.com/forums/dungeons-dragons-discussion/homebrew-house-rules/131411-a-homebrewers-how-to-faq).