I'm trying to use the homebrew tools to set up a second version of my club +1 to factor in the bonuses from Shillelagh, but I don't see a drop down on the magic weapon page where I can specify which stat to use for attack and damage. Is there a way to do this that I'm not seeing? I tried looking through the modifier section, but nothing stood out.

How do they do this for Hexblade Warlocks?

Edit: The actual Shillelagh spell line on the character sheet lists a To Hit, but it appears to just use the spell attack bonus, which isn't really the same as using your spellcasting modifier in place of the strength modifier. For example, a Druid using a Club +1 should get the Wis Mod + Magic Bonus.

The Spell Attack Modifier is the same thing, just without the bonus from the Magic Weapon. You can simply customize the action directly on the character sheet to add the +1 to the Attack and Damage rolls for the action granted by the spell.

While the numbers tend to be equal, thinking them "the same thing" creates issues like we have here where weapon magic bonus isn't factored in attack and damage. Shillelagh isn't really doing what it's supposed to do; it's just hacked in a way that works in most cases.

I've tried making a custom weapon attack to represent the Shillelagh-powered club, but I have an issue where adding the "Fixed Value" only adds it to the Damage and not the To Hit.

And, yeah, could give Shillelagh itself an override to match the values for using on my club, but then I'd have to undo it if I ever used it on anything other than my Club +1. It's also just weird that the To Hit and Damage are set up on the spell action itself, when the spell itself doesn't do any damage.

Customizing the club's attack itself doesn't work because there doesn't seem to be an option to change the die size for damage. I wouldn't want to have to change it every time based on it's state anyways.

I've also tried to homebrew a magic item that would be the Club +1, but with d8 for damage and uses my spellcasting modifier instead of Strength to attack and damage, but there seem to be no way to edit that last bit. I thought I might have had it when I used "Replace Damage Type- Bludgeoning; d8; WIS", but that doesn't seem to make any difference in the weapon when it's on my character.

No, it doesn’t really do what it’s supposed to do. And yes, it is just hacked in a way that works for almost everyone. And no, none of those other methods will work, the best you can do is customize to action added by the spell. 

The spell cannot actually interact with the weapons. Just like feats don’t interact with the weapons themselves, which is why when you use Polearm Master with a +1 Pike you have the exact same issue.

Luckilly, they did give us a way to customize those generic actions that get added by spells and feats. We can customize the action to account for weapons with Magic bonuses. And yes, we have to remember to take those bonuses away if we switch weapons, but that’s still a bagillian times easier than pen and paper.