Darrell Frey

First of all, a bioshelter is a solar greenhouse managed as an indoor ecosystem. habitat, including flowers blooming all year, provide habitat for predatory insects to thrive. Ground beetles, spiders, toads and other predators may also join the ecosystem. A diverse mix of crops, and human control of  crops, habitat, temperature, humidity and light levels help maintain the system.
advice;
plan and design ahead, study the site, the climate, a diverse set of crops to suit the nearby markets,. Design your bioshelter and other season extenders to meet the long term needs of multiple crops. integrate as many functions as you need into a bioshelter, growing area, potting room, processing kitchen, storage., with the growing area getting priority sun spaces and the rest on north side to help buffer climate in the bioshelter. use functional thermal mass, such as deep planters with rock storage underneath.
draw maps, and designs and tweak them until you get the right  layout and the right integration of systems that suit your needs
the better your advanced planning and budgeting, the more success you will have.

I definitely had weed problems. Many of course were useful and incorporated into the salad mix, amaranth, lambsquarters, wood sorrel, sheep sorrel, purslane, chickweed and dandelion. Our biggest problem was quack grass. Galinsoga ws also a problem.
One year I fenced 50 hens into a 500 sq ft area and they cleared it out nicely, but I could not do that on most gardens on our farm. Crop rotations was a good solution. We would mulch long season crops  heavy with straw. and follow them with short season crops like salad mixes and lettuce that we did not mulch. if we tried to keep beds mulched multiple years, voles would move in.
So we would till and rake out grass roots, then plant short season crops, as weeds began to return, we rotate into a mulched crop. them more short season crops. A 3 tine cultivator was used to help pull up grass roots, and a stirrup hoe  to weed between rows across the beds.  
I also suggest Jean Martin's  ( The Market Gardener, New Society Publishing )method of  smothering the weeds with a large tarp for a few weeks before planting.
winter cover crops, also can help.

solar greenhouse design involves: deciding how warm the growing area needs to stay, as in always frost free? warmer, light frost ok maybe? then decide how much space you want to enclose. aggle glazing to catch the sun at the time of year you will be using space. Determine how much sunlight will enter your glazing, and determine if you have capacity to store excess heat in soil or rocks under soil. The figure out if you can insulate non glazed areas. a structure set into ground is preferred as the ground is a stabilizer of temperature. then look at heat gain vs heat loss at night and decide if you need back up heat, such as compost, wood stove or such

Garfield Farm did need permits to build the bioshelter, and they did also need to purchase the land from the city.
We are teaching a PDC in the Pittsburgh area this winter on weekends beginning in January. Check out threesisterspermaculture.com for details

the best advice is to study your site and develop clear objectives and plans before you begin to establish things. Especially when planting  trees nd building structures. Be sure all access paths, water management systems and future development are considered as best as you are able. this will save a lot of troubles later and help you proceed confidently with your plans

miner's lettuce, in Pennsylvania, is productive as a winter coldframe and greenhouse crop from November through late spring. We add a lot to salad mixes. It self seed well and comes up again in the fall if left to self seed in a cold frame

At Three Sisters Farm our main crop was a Salad of the Season. It always had a base of lettuce with 12- 20 other seasonal  greens. they diversity of ingredients allowed us to keep the restaurants interest, and allow for some crop failures to not effect the end product. nhef's want consistent quality  and consistent deliveries. For 25 years, 30 weeks of the year we mixed salad on Wednesday night and delivered it Thursday morning. Other crops included high value herbs, edible flowers and a full range of vegetables. Crop diversity is essential for good rotations
set up appointments in advance of sales calls, take samples of your produce and work with them to develop crop mixes to suit there needs. But restaurants do close, and chefs change jobs, so have a diverse client list as well

I retired from active sales of produce in 2014, after 25 years of market gardening. Our bioshelter does need some upgrades, like it's time to replace the glazing and roofing shingles. But it servered us well all these years. Currently I just harvest some herbs, flowers and greens for personal use and harvest the perennial fruits as well.
I have had the privilege to work at Garfield Community Farm and their bioshelter in Pittsburgh in recent years. Their bioshelter is much smaller than mine at Three Sisters Farm but it suits their needs well. see Garfieldcommunityfarm.com
for more info on that.

Jennifer,
You certainly do not to incorporate animals in a bioshelter. We usually had chickens living in a corner of the building, but not always. The term bioshelter describes the management of an indoor ecosystem. Habitat, as in flowering plants, is maintained to support beneficial insects to control pests.   Often toads and tree frogs would venture inside to live there and hunt for insects and they are welcome members of the bioshelter ecosystem.
Hot compost can also be made with plant material and food wastes without manures if you so chose.

I am not familiar with the smell produced by aquaponics, but I do suggest incorporating mass into the greenhouse to stabilize temperatures. A deep growing bed made of concrete block with rock storage underneath a deep layer of soil has multiple benefits. Air circulated from aquaponics area and the greenhouse will condense in the rock storage and help dehumidify the rest of the system. Be sure to allow for adequate ventilation of the greenhouse in summer!  Passive roof vents are the best options and they should be sized to maintain the airflow and desired temperatures in summer.
The deep soil beds provide a year round growing space and provide thermal mass to help stabilize the greenhouse temperature