Adding homebrew subclasses and a few of them have "if they already have proficiency in said skill they can add double proficiency" is there a way to upgrade proficiency to expertise through homebrew subclass options? or do i just need to have a different option for expertise for the player to choose

Quote from glassfalcon1>>

is there a way to upgrade proficiency to expertise through homebrew subclass options? or do i just need to have a different option for expertise for the player to choose

You just said the same thing twice in different ways.

Yes, make one Option that would grant proficiency and another Option that would grant Expertise. (Don’t use the “Twice Proficiency” Modifier, use “Expertise” instead or else it’ll let them replace the original choice with an extra freebie.)

What I meant was if I could just have one option that if the character already has proficiency in that skill through another source the system would upgrade it to Expertise and just give proficiency if they don't

or do I need to have two choices one regular proficiency and one Expertise for the player to choose from 

Quote from glassfalcon1 >>

What I meant was if I could just have one option that if the character already has proficiency in that skill through another source the system would upgrade it to Expertise and just give proficiency if they don't

 
Ahh, ha ha. You meant “options,” not “Options.” No.

Quote from glassfalcon1 >>

…do I need to have two choices one regular proficiency and one Expertise for the player to choose from 

 
Yes:

Quote from IamSposta >>

Yes, make one Option that would grant proficiency and another Option that would grant Expertise. (Don’t use the “Twice Proficiency” Modifier, use “Expertise” instead or else it’ll let them replace the original choice with an extra freebie.)

So this means that if the character doesn't have proficiency already, the system wouldn't actually prevent them from choosing expertise; it'd be "honor system". Correct?

Yeah Unfortunately, there still isn't a way that i can see to do this

I did it and sort of got it to work, except it seems like the character builder is confused because when I pick one of the options on my character, it still says I haven't even though it gave me the thing. and then when I try to change which option I'm taking, instead of changing it, it adds an additional option. So now it's like my character has deception proficiency + deception proficiency + deception expertise + deception proficiency and I don't know how to remove them...

You must have set something up funky in the ‘brewer. I gave a full walkthrough on how to properly set up Options in the Subclasses & Races FAQ #1: (https://www.dndbeyond.com/forums/dungeons-dragons-discussion/homebrew-house-rules/131411-a-homebrewers-how-to-faq).

There is a modifier Expertise -> Choose Rogue Expertise which should only allow selection of an existing skill proficiency, I believe this is what all existing features that let you pick an expertise currently use, though it will also allow for selecting thieves' tools which you may or may not want.

You could structure this using a sub-class option, with one option granting the modifier Proficiency -> Choose a Skill, and the other granting Expertise -> Choose Rogue Expertise; this way the player can select either one skill to gain proficiency, or one proficient skill to gain expertise, so in this way the condition is properly enforced.

But this will only work for you if you're happy to grant either any skill at all (or one of the other "Choose a [blah] skill" lists) or expertise in any existing skill proficiency, there's no way to narrow it further without doing individual options and the honour system.