Hi, I'm Robert and I'll be helping you with your financial software question.
If you use the place as a second home-rather than renting it out-interest on the mortgage is deductible within the same limits as the interest on the mortgage on your first home.
You can write off 100 percent of the interest you pay on up to $1.1 million of debt secured by your first and second homes and used to acquire or improve the properties. (That's a total of $1.1 million of debt, not $1.1 million on each home.) The rules that apply if you rent out the place are discussed later.
I believe that you could use either as the primary residence. Normally it would be the one that you stayed in for more months but in this case I don't think it would make any difference but I would choose the more valuable house as the primary.
I could not tell you whether it is better to file separately you would have to try it both ways and see which saves you more.
I am in the financial software department here, I can tell you some basic stuff and deal with the software. For tax advice like that i have to send you to the accounting people