You can build farm plots above ground, if you do so, you can plant above plants.
So, if you gathered a shrub, let's say rat weed, you can build a farm plot on grass (above ground) to cultivate it. You can then build a wall and a roof around and above your farm, creating a greenhouse.
For wood, well, i don't want to spoiler too much (i guess you are pretty new to DF), so just so much: there are 'trees' that grow underground and you usually find them if you dig a bit deeper... (sometimes there aren't any, but for maps created with the default values, that is very rare).
And a third possiblity, you can dig a bigger moat and a wall to protect an area above ground, a secure place to chop wood and gather plants, above ground farming... Not absotly safe (flying enemies) but pretty safe (depending on the biome you started). If you want to force your dwarfs to keep inside the walls / a specific area,
check out burrows on the wiki. (understanding how burrows and civilian alerts work will make your life a lot easier!)
Beside that, trading with elves (or killing elf merchants) is another way to get wood.
Hunter can become good marksdwarfs, hunting is a good training for archery that also provides food, bones to craft arrows and leather... so you may don't want to sacrifice your hunters (burrows can help to mark a specific area for hunting). If you create a squad out of your hunters, you can force them to equip better armor (if you have any) and free them from training, as they train while hunting.
And yes, ambushes and sieges will leave after some time.