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If you can run your 12v systems even when the converter is not charging - meaning, if your batteries power your 12v system on their own - then your internal 12v system is connected to the batteries by some other pathway besides the converter-to-fusebox pathway. Most RV's are wired this way.
(If the only way you can get 12v service inside your RV is when your converter is actively charging, then this won't be true, and you may need to rewire a bit.)
So, barring weird wiring, you should be okay to wire the converter directly to the batteries. Wiring the converter output to the fuse panel means you're trying to force too many amps back down some smaller fuse-panel-to-battery wires.