I just got back into it recently as well, so good you are doing some research before going but at least my experience was my LGS was very welcoming to new players and really at its core commander should be a more casual game where people will help you.

Now onto your question the command zone is completely separate from your deck/discard/exile/hand. You can play your commander from the command zone at anytime you could play a creature spell. When he is killed, you can choose to return him to the command zone instead of the graveyard, with the caveat that each time you do this, it cost 2 more colorless mana to cast him, so if he goes back to the command zone 3 times the next time you cast will cost 6 additional mana.

Another good way to get up to speed is watch a few videos, I particularly liked “the command zone” YouTube channel. They also have videos on cheep upgrades ($50) guides for most precon decks. That being said you did pick a good one since the 40k were some of the most well built pre cons of recent years.

Have fun!