i have sold a lot of TICs in the last 10 years and here is how some past clients have done it (I'm going to keep it simple).
3 unit building, 4200 Square feet
Top: 1600 SqFt 38.09%
Middle: 1330 SqFt 31.66%
Bottom: 1270 SqFt 30.23%
2 unit building 3000 SqFt
Top: 1700 SqFt 56.66%
Bottom: 1300 SqFt 43.34%
That is the most simplistic explanation of percentage ownership. Hypothetically, lets say it is a building with no parking. That is the most simplistic for my examples. Each unit gets one vote post conversion, blah, blah, blah.
If you're purchasing a 2 unit building and yours is $500K, you put $300K down, your partner $550K upstairs puts 165K down(30%) and you have one loan your ownership of the structure does not change(you have more equity). If you get a fractional loan (which I don't like) then down payments and loan amounts are irrelevant(basically... for the quick Trulia answer) as the bank (i.e Bank of Marin) looks at them as 3 separate units with separate loans. Your structural percentage still doesn't change.
In San Francisco, the SFAR purchase contract has a section for you to outline that the property is a TIC and the percentages are to be designated in the contract. Hopefully whomever set up the original listing agreement measured the units and outlined the square footages and outlined each units' percentage of the whole.
If you are purchasing a 2 unit building and you get one loan, both partners are ultimately responsible for the loan. It is tricky when you get into partnership on a building. You must investigate each other's financials and be aware each other's intentions and abilities. I have put people together from scratch and rescued a failing TIC by bringing in a new capable buyer. I have seen it from all angles.
My suggestion to you is to get a good TIC agreement. Hire good attorneys (DON'T GO CHEAP!) Herzog, Sirkin, etc.. stick with known entities who know what their doing. Just because your cousin's best friend's sister's husband is a real estate attorney in Fresno... San Francisco and TICs are a different animal.
This is brain surgery... and you don't want to hire a dentist.
Lastly, I live by the philosophy that you should be excited that you are buying a new home. It's a new and exciting adventure. If you can't sleep while you are in escrow, wake up uneasy with 35 questions and/or doubts. A TIC purchase may not be the right transaction for you.
Most likely you have a competent agent. Take advantage of their knowledge and expertise. Hopefully they have done a TIC transaction in the past and know the challenges. Most companies here in the city are familiar with TIC transactions; make sure if they(your Agent) needs assistance they are relying on their Broker. Rely on them to protect your interests. That is their job. Let them do the leg work for you and get your questions answered. That's what we get paid for.
Best of luck to you. Please feel free to contact me directly (415)341-8881 if I can assist you in any way.