Yes, you can claim a credit for a qualified energy efficient roof because of the new purchase and installation, during 2016 on your primary residence. You won't get higher limitations in 2016 because of having two homes. Also, even if you've used the maximum of the credit in prior years, there's credit allocable to expenses for 2016 ($300-$500)
See more at the IRS HERE. If this wasn't what you meant, let me know if you have more questions.