So I am going to start with loan program type. There are two main loans I would look at FHA and Freddie Mac Home Possible.
FHA requires 3.5% down with a minimum 580 credit score, most companies have an overlay mine is no exception our minimum score is 620. The loan limit for a Duplex in Seguin, TX is $516,750. This allows a non-occupying Co-borrower. However FHA also will have Mortgage insurance for the life of the loan.
Freddie Max requires 5% down and the loan Limit is $702,000. This also allows for a non-occupying Co-borrower. As this is a conventional loan you will have mortgage insurance until the Loan-to-Value reaches 80%. According to Home Possible guidelines the borrower may only have ownership interest in in 2 financed residential properties including the subject property.
As David above me said, there will be a single mortgage that is then split by the borrowers how they choose. You can assign the percentage of ownership between the parties. At the end of the year the CPA will prepare taxes based on ownership percentage.
Best of Luck!