Harmonic Ascension uses Hardcore Questing Mod, Minetweaker and Modtweaker to arrange the mods in a semi-linear fashion. Don't worry, if you'd rather play in sandbox mode, select the optional configs in the sidebar.
There will be two reputation types: Science & Magic. Doing quests will give you rewards, and reputation in these two areas. Some quests aren't clearly either and so may give you some mix of their reputation
When you get enough Science you advance Science Tiers.
When you get enough Magic you advance Magic Tiers.
When your Magic > Science x (Difficulty multiplier Normal is 2) or the reverse is true, bad things start happening
At different tiers you gain access to crafting recipies of mods suited to that Tier.
Survival, Hunting, and Merchant quests are the first three quest groups.
Survival is intended to bootstrap people into the Primitive or Classical progress levels.
Hunting is intended to encourage adventuring, and help balance out reputation.
Merchant is intended to reduce grindy repetition, at the cost of money (emeralds or IC2 currency) and leaning more towards the reputation of the side the item helps.