To answer your question, all of these loans, including things like credit card debt, or other bills can be rolled into your new mortgage.
Since you have a 2nd Mortgage @ 2%, I would ask them, if they will subordinate the debt to a new lender, or mortgage. And than, if given the go-ahead, leave it in place. That 2% Rate is a good deal, on a relatively big balance -- and you might as well, keep it as low as possible.
The Mortgage with Citizens Bank is bizarre. Were you previously delinquent on it? Some lenders would charge those off after six-months of non-payment, while some didn't -- but I find it odd that they told you, not to pay it anymore.
If you really want my advice, I would try and ask for a lien-release. What you want to do, is get a printed copy of the security instrument/mortgage/lien recorded against your home, and fax them a copy of it to their Lien Release Department. You'll also want to include a personal note saying, this debt no longer exists, and the lien needs to be removed. Sometimes, you can get a copy of this document - from your Clerk of Court or County Register of Deeds website.
I recently had luck doing this with someone's Region's Bank Loan. And the worst they could say is - No. You still owe it.
Which brings me to my last bit of advice. You could try to settle the account for $15,000 or $20,000 -- instead of the full amount. They could be paid off for release in their interest in the property, via your Refinance. You just need a good loan officer handing your file. I would do this last, and see if you can get them to release it without $$$.