Not possible to change them after it starts, you can only set the percentage at the beginning. But now that I think about it, it may be possible to add that to the July 1 editing (although it wouldn't affect player generation until the following year.)
The age setting has to stay fixed for the time being so the top-level teams can send their (signed) young players down, and as a side effect it allows the minor league to sign some younger guys as well. Effectively, it works a little like the later years of the old International Hockey League, where it's both a farm league and grabs some prospects on its own as well. It's going to be a little complicated to fix that - basically, we'd need to make an equivalent of the NHL-CHL agreement in the custom games so the 18/19-year olds signed to the top level teams can be sent back to junior. Problem is, that requires a bunch of messy hardcoding to work in the modern games, and if we implement it in custom it's going to be really inflexible and unchangeable, which isn't really the direction we should be going in for a game mode that's supposed to be highly editable. I'll try to figure out some alternative, like allowing all junior teams to function as farm teams for the NHL, but that's going to have its own issues to work out.
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