I've done this a fair few times and I'm generally a big fan of the idea.
I think there are a number of ways to approach it and if any of these is a method you are happy with then it's completely worth it (play what you love and all that).
Approaches:
1. Have two completely independent decks with either no crossover or multiple copies of cards for each deck.This is great for convenience but potentially bad for your wallet and/or the power level of the deck. It will feel bad if you are left in a position where one deck is running a sub par mana base compared to the other (unless of course, this is by design to keep it at a certain power level).
Alternatively, this can also be a fun deck building restriction if you want to push the boundaries and
explore cards outside of the obvious.
2. Have a base deck that is consistent for both (lands, ramp, draw) and swap out key cards.This is great for your wallet but a can be pain in the ass to manage, especially if you want to play both decks on the same night. It's not insurmountable, but does require some organisation.
3. Keep one deck as the "proper" deck and proxy any crossover cards you want in both decks.This is the best of both worlds providing you don't play with any pissy little babies who care about proxying a card that you already own for the sake of convenience.
I've tended to go with the last option for mine when I've done this. I've built multiple versions of
Queen Marchesa and
Extus, Oriq Overlord but I don't want to buy fetches and shocks and talismans and signets and whatever for 4 decks, so I have my main deck (Marchesa Aristocrats) and have printed out proxies of all the staples that I want across multiple decks.
I toyed with the idea of a Mardu base that I swap out each time depending on the deck, but Marchesa aristocrats wants a very different amount of lands and ramp compared to
Piru, the Volatile so ultimately I decided to
scrap the idea and proxy instead, which my playgroup is totally cool with.
Generally speaking though, I think it's a great idea if you can manage it properly or find a
balance you are happy with. Playing what you love is the best part of EDH, so having a much loved commander built with two different much loved archetypes is wonderful.