I play with the Variant where there are 2 Ally decks. The first deck (i.e. the Town Deck) has 11 Allies that are there only for the purposes of removal via the Terror Track. The 2nd deck is the so-called "Citizen's Deck", and I place 11 more Allies in there for use with Ma's Boarding House etc . I currently have 33 Allies in my collection to randomly draw from (many of them fan-based).

My question is: where do you recommend I should take Charlie's Ally from & should it be a choice or a random draw?

I'd suggest Charlie draws from the 11-card deck, as he would do in every regular Arkham game (and possibly discard 2 allies from the other deck, just to grant the starting conditions are still proportionate with the original intent)

The only thing I use "citizen's deck" for is if a specifically-named ally is granted from an encounter and it's not available in the main deck. If I get one at random or one of my choice, it comes from the main deck.

Also, whenever an ally is removed from the game, I remove one from the main deck and three from the Citizen deck.

Lastly, when I take one from the citizen deck, I randomly move one from the main deck into the Citizen deck, ensuring there aren't more than 11 allies in the game.

I'd suggest Charlie draws from the 11-card deck, as he would do in every regular Arkham game (and possibly discard 2 allies from the other deck, just to grant the starting conditions are still proportionate with the original intent)

Good suggestion.

The only thing I use "citizen's deck" for is if a specifically-named ally is granted from an encounter and it's not available in the main deck. If I get one at random or one of my choice, it comes from the main deck.

Also, whenever an ally is removed from the game, I remove one from the main deck and three from the Citizen deck.

Lastly, when I take one from the citizen deck, I randomly move one from the main deck into the Citizen deck, ensuring there aren't more than 11 allies in the game.

Even better suggestion.