I cluster workcenters.
Take for instance, the following inter-related industries:
Farming
Threshing
Milling
Weaving
Dying
Jewel encrusting
Metal decoration
I like to establish work flow diagrams on paper to understand the connections between industries, so that workcenters and intermediate stockpiles function efficiently.
So, for the above:
Farming (ropereed/pigtail)->custom food stockpile-> farmer's workshop(threshing)->thread stockpile
From there we have either:
Thread stockpile->dyer->thread stockpile->loom->cloth stockpile
Thread stockpile->loom->cloth stockpile->dyer->cloth stockpile
Then we have:
Cloth pile-> clothier->finished goods->clothier (image)->finished goods->jeweler(encrust)->finished goods->forge (decorate)->finished goods->trade depot
These manufacturing processes need continual and cheap access to raw materials. So, consider what each one needs.
Farm plot needs a food stockpile to quickly get crops in to minimize crop loss, and needs a seed stockpile to maximize planting speed.
Farmer's workshop can be a dedicated process in several sites in the fortress. Here, we grow fiber and dye only at the farm plot. (Pigtail/ropereed/bladeweed/dimplecup/redroot/etc). Pigtails and ropereeds are alcohol sources, so an expedient path to the fortress pantry and the brewery is prudent.
Millers have to take dyestuff raw material to the mill to get dye. Dyers need dye to dye fabric. This means the dyers and the millers have to be in close proximity to each other, and their respective stockpiles.
What I usally end up doing is a multi z-level workshop tower. It has sublevels underground, and vertical levels above. It has duplicate industries converging on the ground floor.
In the sublevels, the deepest level grows pigtails and dimple cups. It stores the raw plant material on the same floor. Right in the middle of the stockpile is a stairwell going up to the next level, which houses threshers, millers and dyers, and their respective stockpiles. The next level up houses the cloth and thread stockpiles. Here is where the looms and clothier shops are.
Next level up contains a magma glassworks, optimally has a sand patch, and contains the gem stockpile, a finished goods stockpile, and a sandbag stockpile. It contains jewelers shops.
Next level up is ground floor. It houses the main food stockpile, the magma metal works, a finished goods and furniture stockpile, the carpenter's shops, the still, and kitchens. Outside the front door is the trade depot.
The above ground layout is the inverse order of the below ground layout for this industry pipeline.
Clothing is created from dyed fabric, enhanced each step, and accumulates on the ground floor near the depot.
I usually use a 4 tower design with distributed central space, and lower central subfloors for the residential district, employing the easy magma access of a volcano.
1 vertical tower pipeline produces fabric, like I listed. Another produces obsidian and rock products, greenglass block, and other glass products. Another stockpiles metal, wood farms and the like. The last is the food production tower, and houses the leatherworks and animal pens as well as the food crop plots.
Entire fortress layout is designed for central workforce deployment, and product flow from the edge of the fortress to the central chamber. Long term "fortress hoarde" (artifacts, super awesome multiple masterpiece quality multiplier goods, etc) goes below the residential district in the central area.
The idea is to exploit that verical distance is shorter than horizontal distance, so that the space between workshops can be reduced drastically, increasing speed of hauler job completion.
I am still experimenting half-assedly with improving performance, but that's kinda boring.
Some experiments with direct gangways between production towers (getting obsidian cabochons from the obsidian reactor tower to the clothier tower without going through the ground floor, etc.)
My current project is a departure from efficiency for pure aesthetic quality, being a mega construction.