Embark: I use the defaults because I'm lazy.
Farming: I usually have about 6-8 plots of 4x4 size, half underground and half surface. I can't always remember which crops are which, so aboveground I generally just plant the berries. I do a little local (d)esignate-(p)lant gathering in the first year to bootstrap the aboveground plots. Belowground, the first plot obviously gets plump helmets, then I usually do sweet pods and cave wheat in the next plots to get more booze variety. Obviously all the subterranean plots are set to plump helmets in the off seasons. This does require a fair amount of farm labor; I generally turn on farming for every brown-class migrant I get - soapmaker becomes farmer, lyemaker becomes farmer, milker becomes farmer, etc.
Brewing: I usually have just 1 carpenter shop, set to repeat bed/bin/barrel, which seems to be able to keep up with one still doing brew drink on repeat. I'll often keep a small food stockpile set to take only raw plants nearby, and a furniture stockpile set to keep only barrels. If the booze runs low it's usually because the brew job stopped because the barrels ran out because of a problem in the wood pipeline.
Fishing: The process-fish order does get cancelled (for lack of fish) more often than the brewing task does, but if you remember to check every season or so, it's fairly productive. My solution to the refuse problem is usually to have workshops and the main dining hall on one level, stairs down from each of those to a connecting tunnel on the next level down, and a big refuse storeroom (10x10 to start, growing as it fills up) a little ways off that tunnel, midway between the two. Short walk from the dinner table to the scrap heap, short walk from the craftdwarf's workshop to the scrap heap.
Hunting/Meat: Since immigrant hunters come with equipment, I just leave them to their task and hope for the best rather than trying to train & equip new ones. Their productivity and life expectancy is entirely dependent on what kind of local wildlife you have. I alternate training war dogs and hunting dogs, so any hunters that survive a season or two generally get a little buddy to improve their odds - (v)iew dwarf, (p)references, (e) work dogs, if you didn't know about that one. I butcher the fuck out of kittens, foals, calves, etc, and request every kind of meat from traders and buy it all, which means plenty of meat available -- not that you really need meat to run a fort.