The pack centres around growing your resources, and getting access to seeds. Plants need training to reach full effectiveness. Thus, most of your effort is spent improving seeds.
Fully trained (10,10,10) seeds grow multiple times faster and produce 4 times as much as the basic 1,1,1 seeds. Always put the effort into training. A decent training rig in the current game is a long strip of soil (10-12 long, for type see below) with cross-pollinator crops (i.e. two crops) in each. Plant your base seeds at one end, harvest your improved seeds at the other.
Sprinkler systems make a huge difference to growth rates. With fully developed plants, I don't find that really important, but for crossing and training plants, a sprinkler watering system is so nice. A single sprinkler head does a 7x7 square.
Soils: Non-magical crops can grow on dirt, but magical flowers (for botania) need untilled garden soil, while magical crops need tilled garden soil. Mushrooms need mycelium. Cactus needs sand. Sugarcane can grow on sand or dirt. This isn't always obvious.
Start making garden soil fairly early. It takes a lot of composting and you need a lot of it. It is also not the same as regular dirt in a couple of important ways: 1) It doesn't follow the hydration rules for normal soil. 2) IT CANNOT BE UNTILLED---break it and you get a tilled block. This means only flowers or magical crops. You can't switch easily.
Fertilizer: all flowers and regular crops (vanilla and agricraft) take bone meal, which is very easy to produce. All the magic crops (essence plants and it's descendants) need magical fertilizer, which is quite a bit harder to make.
For crossbreeding new seeds, make a two by two pattern, planting the parents at opposite corners. This allows two chances for a new type of seed to breed. You can sometimes use the dirt type to force a cross to happen (e.g. when breeding sugarcane, use sand to force the cross).
Always make sure you have an extra seed for every plant. Because I'm paranoid, I have four, three in a chest by the fields, the other in an underground obsidian vault, in a chest covered in water.
As for how many plants you need ultimately (assuming all are 10,10,10):
For Botania flowers and for the ingredients for magical food, I find a single one of each is more than enough for magical flower production or for making more than enough food. These are easy to grow with vanilla bonemeal anyway.
For the magical crops, I'm finding a 4x4, 16 plants is enough for most crops. That gives exactly a stack of essence each harvest. I have a double plot of essence seeds to make all the essence I need though. I don't fertilize or water these. A single day cycle is enough for the crop to regenerate, with no extra help.