I recently moved out of my upside down mortgage and about to attempt a short sale. I moved to another state and got a small sign on bonus of 5k, plus another 5k three months from now. I have a BoA bank account and my home loan is through BoA. My question is can they see my balance, and will they deny me a short sale because of it, and more importantly, can they take any of that money?

I'm thinking the mortgage department has no rights to my balance without me providing it, and I'm almost certain they cannot touch my money. Thoughts?

They can definately see AND take your money. Move it to another bank ASAP!

right of offset - check your account terms, but generally if you owe the bank money, they can take it from your deposit accounts without notice.