I use Quicken and I love everything about it. The website is awesome, everything is spelled out for you, they have so many loan options and paying extra whenever you want is super easy. I can't recommend it enough.
Just be sure it's still a qualified home loan, so you can deduct the interest from your taxes. (Although with the tax codes changes, it may not matter anymore.)
The only time it makes sense to roll short-term debt into long term debt is if you have really high interest rates, which makes the paying off the short-term debt nearly impossible.