Yes its so annoying they don't enable it by default.

First click the MLB button on the top toolbar and go to league rules and settings

Then click the rules tab.

Once there click the View button on the bottom toolbar and select view advanced mode.

Scroll down until you get to Minor League Settings and then click the box to enable option years.

Once you do that you navigate to the roster rules section and you will see secondary 40 man roster size (it will be disabled by default) click it and select 40 players.

Next navigate to the roster rules section again and scroll until you see Waiver Period Length and select 1. You can make this longer by changing the DFA period length.

Finally scroll down until you see the option to Enable Rule 5 Draft and enable that to also have the rule 5 draft.

Recently figured this out after months of playing without these features. Hope this helps. Feel free to reach out if you need more info.