You can either have a shared draft or have each league use their own draft.
What you want to do depends a lot on how you setup your leagues and what you want to achieve. The main thing to consider is the talent difference between your leagues. You can do anything from all leagues being MLB equivalent to MLB > AAA > AA> etc. or whatever else you want. You can literally set the talent level (player creation modifiers) to whatever you want.
The draft isn’t going to “mess up” your league. You just need to set things up to your expectations/goals.
If you’ve got questions fire away…
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