I sent NW_Kohaku a link to a short book on organic composting just a little bit ago. (Free on gutenberg!)
My mom also does extensive organic horticulture, and has for years. I haven't had the opportunity to read this thread properly yet, but will offer advice after doing so too.
Currently too busy making industrial blueprints for my employer.
OK, reading the first bits with a quick glance, basically you need to impose limits without breaking the system spectacularly. This means you need crop management.
An example of modern failures of crop management, is the over-use of nitrogen fertilizers. They allow explosive growth of green plants, by permiting ready protein synthesis, but this also affects soil microbes, which use the nitrogen to destroy the soil's carbon based organic sponge, or humus. This results in a lower and lower capacity for the soil to retain and provide nutrients over time, resulting in less and less nutritious produce over time. Ideally, farmers would replenish this lost humus through liberal application of compost, but supplying compost at those scales to sustain massive intensive agriculture is simply not economically feasible. This has resulted in the steady decline of fertility in modern agricultural regions over time. In short, the "green revolution" using synthetic fertilizers is simply not sustainable.
For a more historically accurate picture, we can look at crops as being one of 3 basic types: soil buildng, soil neutral, and soil depleting.
Legumes and certain grasses are soil building. These are things like clover, alfalfa, and tall prarie grasses. These plant forms either fixate soil nutrients directly, such as legumes, or produce copious amounts of organic sponge raw materials, like gras straw and as such, build up the sod layer, making it more useful for agriculture.
Soil neutral plants only make use of an established sod layer, but don't disrupt the soil's equilibrium in a serious fashion. Most weed plants and leafy herb type plants are of this variety. They have requirements for different types of soils, (for instance, sorrels and mallows tend to thrive on poor soils, while cooking herb plants prefer richer soils.) But don't really change the biome significantly, and form a homeostasis with their environment when competing with other similar species in the ecosystem.
Soil depleting plants essentially "rape" the soil, draining it of vital reserves of nutrition, and force the farmer to have to correct the imbalance by growing a soil improving crop soon after. These are things like cotton, especially, but also includes things like major vegetables, and some cereal grain crops.
As previously stated, the major modern deleterious factor is the destruction of humus in the soil by intensive cultivation coupled with nitrogen fertilizers. All plants require nitrogen to produce protiens within their cells, which is essential for them to live. Nitrogen from the air won't do, because it is too difficult to overcome the high energy triple bond of the N2 dimer, at least fr the plant. This is where soil building plants like clover and alfalfa come into play. As legumes, they serve as a symbiont for a very vital soil microbial fauna that is able to take nitrogen dimers from the atmosphere, and combine it with oxygen and alkaline earth ions to produce nitrate compounds, which they share with their symbiotic plant partner. (The plant provides them with a stable growing environment, reliable moisture supplies, and simple sugars for food.) The maximal benefit of these crops comes from composting the while plant bodies of these plants over the year, by tilling the plants under at the end of the season, and then allowing the field to lie fallow. This returns the nitrogen and soil humus reserves to the soil, with a surplus from the fixation processes of the legumes.
Depending on the aggressiveness of the depletions of the actual crops grown per crop, build, fallow cycle, differing amounts of building and fallowing will be required for sustained agriculture.
Coupling that with seasonal restrictions, and entire year fallowing times, ad you will quickly find that you need much more cropland that DF currently requires to provide stable food production in the long run, without destroying the soil. (Completely depleted soil is almost impossible to get started again, without very intensive and laborious efforts. In fact, fully delepted soils won't even grow weeds for cover, and will become blowing deserts!)
What needs to be done here, is to segregate surface crop cultivation, from subsurface crop cultivation, because the type of organism cultivated in those growing conditions have VERY VERY different requirements. Up until now, I have been referring only to surface horticulture.
Mycological species are NEVER producers. *all* species are soil depleters! Since they do not get any of their energy from sunlight, 100% of their biological energy comes from the decomposition of already existing organic materials.
In the case of DF, the native biome for these organisms are vast underground cavern systems with interspersed volcanic vents and cavern lakes. As such, the primary producers of this environment are likely to be autochemotrophs, which as far as I know, are all monocellular. These organisms usually have a sulfur respiraton cycle, and make use of mineral and geochemical energy sources to produce primary nutrients, and build up organic humus of sorts through their accumulation, and decay on the bottoms of these cavern system lakes and rivers. Periodic flooding must somehow trasport these organically rich silt deposits onto the cavern layers adjacent, where secondary fungiforms make use of it to produce food products for cavern organisms, who transport the nutrients further afeild via their droppings. Each time, energy will be lost from the natual processes of the organisms involved, so the primary concentration of nutriton would be found in the cavern lakes and rivers as silt.
Sustainable agriculture of subterrene crops would therefore require either periodical inundations of the croplands with fresh layers of cavern silt, or direct introduction of organic materials from the surface, such as compost, to sustain the nutritional and biological requirements of these crops. This means that unless very elaborate methods to artificially induce seasonal flooding with cavern water sources is enacted, underground crop production would be tied to the hip of surplus nutrients produced above ground, and transported below, to be sustainable.
We will have to conjure up numbers for the rates of consumption, ad production of these nutrients to establish a growing chart.