So if I complete the main quest in preseason and mark it complete for my season 1 character, are all the side quests still going to be available?
Or will they be marked as complete as well?
You are actually asking two separate questions. You will not be able to do side quests with your seasonal character unless they are unique to the seasons. You will be able to do any side quests, Lilith statues, renown with any “main” character. However, certain things will have to be done by each character - like side quests but certain other things (like Lilith statues) are unlocked for each character across the realm as well as certain things are unlocked for just your account (like renown). So, person A finds a Lilith statue and you get the stat raise or whatever the statue does. This process starts over when you create a season character but, when your character flips over to the “main” realm at the end of the season, it becomes a “main” character and gets all of those bonuses but loses the season bonuses. Hopefully, this helps more than it confuses.
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Makes perfect sense: the side quests from the main game are not applicable to seasons. Thanks. 
They are called sidequests because they aren’t a part of the main campaign.