The 'custom settings' are not actually the settings of an existing stockpile, they're new settings to use for a stockpile you are creating. I have to say I never use them as I rather just designate the main kind (e.g. furniture, food, etc) and then use the settings menu to add additional types as needed.
To see and change the settings of an existing stockpile, use (q)uery - (s)ettings on the stockpile. These settings should not change unless you change them.
As to the food and drinks, it is actually fairly easy to set up farming in df2012, but I know that it took me a couple of forts to get it right initially.
Some tips:
1) only use plump helmets initially. They are the easiest and most versatile plant, they grow all seasons and can be eaten raw, cooked (but you don't want that), and distilled, and don't need any complex processing
2) you don't really need a kitchen for a while. A 4x4 plump helmet plot and a still should be able to get you going for a long time. Once you have the production going you can add a kitchen to get more variety in there.
3) stills need barrels or large pots. I much prefer pots since I always have too much stone and too little wood, but it doesn't really matter. I like making an empty pot stockpile near my kitchen/still to save hauling and to have a visual on how many empties there are left. (furniture storage, forbid types, then manually select to large pot from the rightmost list)
4) as said before, make sure to turn cooking off for plump helmets as that will destroy the seeds. But if you don't have a kitchen it's not really a risk :-)
5) talking about seeds, it is best to have a seed stockpile near your farm that doesn't use bins (food stockpile, block everything, then allow seeds). Make sure to disallow seeds on your main food stockpile. In fact, I usually create 5 stockpiles in my food rooms: seeds, drinks, prepared meals, other food, and empty barrels/pots. This helps keeping track of everything even without a bookkeeper.
If you have a task that needs done but doesn't get done, such as farming, brewing, or woodcutting, go into therapist and see what your farmer etc is doing. If it takes too long, disable hauling on them. If they go to 'no job' while you have a job queued up something is wrong .Check your announcement logs for cancellation messages and make sure that the dwarf can get to the target.
Finally, a really easy way to get more food is to bring chickens or other poultry. Just bring 5 females and a male, and make nest boxes in your crafts workshop, install the nest boxes in a room, and pasture the chickens in the room. That will quickly give you more eggs than you ever need without requiring any maintenance (long term, you need to have a breeding program to replace aging poultry, but the first couple years you'll be fine.