The wiki pages for workshops display which tiles are impassable. If the workshop is available to you (magma versions isn't until you've found some), trying to build one should display the impassable tiles (with the Phoebus tileset they're darker).
One reason for having space between workshop is that they tend to get cluttered, and I suspect cluttering slows down walking speed as well as work speed, but I don't actually know.
I tend to have the farm plots and its production chains on the "upper" floor, since that's the one that's typically farmable (i.e. not stone floor). Beside the farm plot(s) I have an indoor seed only stockpile. Thus, I have the still beside the farm with a stockpile that only takes brewables (including outdoor ones) in between them. Another stockpile is dedicated to pig tails (and hemp... overland crops) for thread production, then a farmer's craftshop to process the plants, a thread quantum stockpile, then a loom and a cloth quantum stockpile, and then a clothier. Since I use DFHAck workflow, I actually create three clothiers, one for each type of cloth (plant, yarn, silk), so I just can restart the production list when enough material has accumulated. If I bothered with milling it would end up here as well, with its own source stockpile. The pressing mess would also end up here, with all the stockpiles required to ensure you didn't just crush your last rock nuts (which I don't grew, since food is not an issue).
On the second level I usually have "ordinary" workshops, with a general quantum stockpile in the middle, with its feeding stockpiles around it, and on the next level the big food stockpile (that excludes brewables/threshables) on one side of the main corridor, the kitchen opposite it, fishery on one side of the kitchen and butcher on the other, tanner beside the butcher (with a raw hide only refuse stockpile), and then the leatherworker beside that. Behind the butcher I place the indoor pen (birds, dogs, typically). Below that I have the mess hall, and below that I have several levels of dorf's accomodations (something like 12-20 a level on each side of a corridor, with staircases at each end). In the completely enclosed courtyard the grazers' pen is located, with a farmer's workshop for shearing/spinning (I've given up milk/cheeze since it's too much work, especially since I have serious food over production as it is, but when I did, I had a separate farmer's workshop for milking/cheezemaking). I also have outdoor farm plots here, and a bit later, when I've got some time, I dig out a little area (from the cliff face I dug into) for outdoor seeds only.