I'm assuming the second battery is now gone, and there's just a big heavy cable sitting there waiting for you.
Whichever fuse box you want to connect to it, the answer is basically "yes". There are two approaches - as bods indicates, a direct connection leaves it connected and active at all times, because not only is it connected to your alternator, but it's connected to the other battery.
An improved method - which will safe-guard your starter battery from possibly going flat - is to put a very heavy relay in place to bring the power to the fuse box on only when the ignition is on (which means, usually, engine running). Poke through the fuse box in the engine bay for a connection that only comes on when the engine is on, and tap into that - it will draw milliamps, so won't affect whatever it is. Connect this to pin 85 of a 120A relay. Pin 86 goes to vehicle body or battery negative. Pin 30 goes to the big heavy cable and pin 87 to the fuse box. Job done. You can use an isolator instead, as bods suggests, they're more expensive but monitor the voltage not just an on-off signal.
The kicker is what you're going to do with the output from the fuse box. If you're going to run accessories from them, you run the risk of flattening the starter battery. An alternative to that is to put a deep cycle battery in where the second cranker came from, still use your fuse box, still use the heavy relay, but this time pin 87 goes to the second battery not the fuse box. The fuse box connects directly to the second battery. This gives you an isolated auxiliary battery for use when camping, without any risk at all to the starter battery.
So, yes what you're suggesting is safe, but depending on what you're trying to do with it, there might be other answers that improve the system even more.
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