The qualifying score is the lowest middle score out of all applicants on the loan, so if you and your fiance are on the loan, and your middle score is higher, then his score would be the qualifying score. The middle score is the median score out of 3 - so someone with 680, 658, and 671 scores would mean the 671 score is the middle score.
Since your fiance makes the income, then he would need to be on the loan. You said he has never done anything to affect his score/credit, do you mean bad? If he's never missed a payment, filed BK, had a tax lien, charged-off account, a collection or a judgment then his score should actually be pretty good - even if he has some credit cards near their limits. Now if he has some of those items I mentioned, your concern about his scores could be justified... but either way, so you are prepared, I would recommend you ask him to check it at a website that will give you the scores that a mortgage lender will use.
Mortgage lenders use FICO scores - as a consumer, other than from a mortgage loan officer, you can only get your FICO score from Equifax & TransUnion from http://www.myfico.com as Experian no longer allows consumers to get their actual FICO score. If you are at a website where you can get all 3 scores, you can be pretty certain that they are not FICO scores but a newer scoring system called Vantage credit scores. Vantage credit scores use a lot of the same information to calculate your score, but it gives different "weight" to different parts of your credit profile, so the credit scores are not the same as your FICO scores. I am not sure why Experian no longer allows consumers to get their FICO score from them, I could only speculate that because consumers are not their clients, creditors are, so that may have played into their decision to prevent consumers from getting it. Whatever the reason, at least you can still get your Equifax & TransUnion FICO scores from that website.
To qualify for FHA financing (one of the easier programs to qualify for, and with low fixed interest rates) most lenders are looking for a 620 or 640 score, but if you don't have much of a down payment and want to qualify for conventional financing, then a 680-720 is generally needed. Still, the higher the scores, the easier an underwriter is going to go on you.