How do I set up an efficient Harvest?
The short answer, at least early game, is "don't worry about it."
Until you expand more, just worry about placing buildings and finishing them off. After unlocking my third or fourth plot of land, I remade my settlement a bit. Arrange the houses and other buildings that don't have active effects in a corner. You won't need to touch them.
In another corner, set up harvesting/farming zones.
I'm dying a lot in Ball x Pit
The most obvious problem might be that you aren't quite ready for the latest stage you unlocked. Sometimes, the difficulty jumps are considerable.
But there might be more to it than just grinding a previous level. The most important check you need to do is in your settlement: have you upgraded your buildings as much as you could?
Press TAB on PC to easily see which buildings are upgradable in Ball x Pit.
After planting quite a few new buildings, I didn't realize that I could get many of them to level 2 and 3. Particularly, the skill scaling buildings. Upgrade everything you can to the max, and all your characters will get extra stats and scaling.
Also consider the fact that some of your characters might be a lot weaker than others; fresh characters starting at level 1 will just have a harder time initially than others.
Boss Fight Tips
They're all different, but the biggest tips I have are:
1. Take your time (there's no limit as far as I know).
2. You can slow down the game speed just for the boss fight. Help yourself dodge those tight bullet hell segments. Also, remember to bait the boss attacks in a certain direction.