I'm just wondering if you have really thought this through? Let me see if I have this straight.
You want to buy a house becuase the location of your fiance's house doesn't suit for work.
Your fiance's house is in negative/no equity.
Your fiance is going to take out a loan to give you money for a deposit so you can buy a house & avoud stamp duty. (Won't go into tax implications of this as well versed already!)
Sorry but this seems like a crazy idea. Your fiance has a mortgage already to pay and you say he has no rental income. He plans to get a loan to give you the deposit, thereby putting himself in more debt? If he had the cash that's one thing......by him borrowing money for deposit, you'll be borrowing a very high % of purchase price. It might be an unpopular opinion, but there's a reason why banks are stricter on LTVs than in the past....
Can you not continue renting (which I assume you are doing), keep saving & get the money for the stamp duty and deposit together, then buy a house together - using both incomes for repayments?? It's above board & would give you more wriggle room. If you say this house is in your name only & you only will make repayments - what happens if you give up work for a while? Will you be able to afford on your own?