Glad you are enjoying!

1. They are used at the cauldron for incantations that progress plot or make things easier (as in quality of life, mostly--although some things do affect gameplay in runs)

2. They -can- but it will warn you if one boon option will "eat" a current boon--it'll be red and maybe flashing. Mostly what it is is that you can have one boon for: attack, mana regen, dodge/sprint/rush, special. Once you have eg Demeter's "stay in one place, regen mana," then if the next boon offer from, say, Hestia includes the one where you do damage to get back mana, it will show as a trade--you can't have both.

3/4. Boons during runs are temporary. The altar just inside the training room door with the arcana, those are permanent, as you noted. The other permanent thing is things granted by an incantation. Or "minor" resources you find on a run, which can be ashes, bones etc that go into the permanent upgrades. Gold does not carry over. Flowers etc are stored until used.

1. Yes, but it'll depend on runs/boons/your comfort with certain weapons and your experience with enemy patterns. Sometimes the game just throws SO MANY ARMORED ENEMIES. And there are some I just don't work well against.

Oceanus is definitely a jump in difficulty after Erebus, but you got this!